RCSB PDB Help
Attribute Details |
Structure Attributes
ID(s) and Keywords
Entry ID(s)
| Attribute | rcsb_entry_container_identifiers.entry_id |
| Description | Entry identifier for the container. |
| Type | string |
| Examples | 4HHB AF_AFP60325F1 MA_MABAKCEPC0019 |
| Iterable | true |
PDB Deposit Group ID(s)
| Attribute | pdbx_deposit_group.group_id |
| Description | A unique identifier for a group of entries deposited as a collection. |
| Type | string |
| Examples | G_1002119 G_1002043 |
| Iterable | true |
Assembly ID(s)
| Attribute | rcsb_assembly_container_identifiers.assembly_id |
| Description | Assembly identifier for the container. |
| Type | string |
| Examples | 1 5 |
PubMed ID
| Attribute | rcsb_pubmed_container_identifiers.pubmed_id |
| Description | UID assigned to each PubMed record. |
| Type | integer |
| Minimum Value | 5 |
| Maximum Value | 39655996 |
| Examples | 15937111 |
| Iterable | true |
EMDB ID(s) for Maps Used in Structure Modeling
| Attribute | rcsb_entry_container_identifiers.emdb_ids |
| Description | List of EMDB identifiers for the 3D electron microscopy density maps used in the production of the structure model. |
| Type | string |
| Examples | EMD-21578 EMD-30168 |
| Iterable | true |
EMDB ID(s) for Related Maps
| Attribute | rcsb_entry_container_identifiers.related_emdb_ids |
| Description | List of EMDB identifiers for the 3D electron microscopy density maps related to the structure model. |
| Type | string |
| Examples | EMD-21578 EMD-30168 |
| Iterable | true |
Accession Code(s) - UniProt
| Attribute | rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_accession |
| Description | Reference database accession code |
| Type | string |
| Nested Attribute | rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_name |
| Nested Attribute Examples | P01308 P0CX43 |
Accession Code(s) - GenBank
| Attribute | rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_accession |
| Description | Reference database accession code |
| Type | string |
| Nested Attribute | rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_name |
| Nested Attribute Examples | 12057205 1329886537 |
Accession Code(s) - NORINE
| Attribute | rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_accession |
| Description | Reference database accession code |
| Type | string |
| Nested Attribute | rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_name |
| Nested Attribute Examples | NOR00033 NOR00972 |
Structure Keywords
| Attribute | struct_keywords.pdbx_keywords |
| Description | Terms characterizing the macromolecular structure. |
| Type | string |
| Examples | DNA RNA T-RNA DNA/RNA RIBOZYME PROTEIN/DNA PROTEIN/RNA PEPTIDE NUCLEIC ACID PEPTIDE NUCLEIC ACID/DNA DNA-BINDING PROTEIN RNA-BINDING PROTEIN |
UniProt Molecule Name
| Attribute | rcsb_uniprot_protein.name.value |
| Description | Name that allows to unambiguously identify a protein. |
| Type | string |
| Examples | Hemoglobin alpha |
Additional Structure Keywords
| Attribute | struct_keywords.text |
| Description | Keywords describing this structure. |
| Type | string |
| Examples | Inhibitor, Complex, Isomerase... serine protease inhibited complex high-resolution refinement |
Entry Group ID(s)
| Attribute | rcsb_entry_group_membership.group_id |
| Description | A unique identifier for a group of entries |
| Type | string |
| Examples | G_1001001 |
Polymer Entity Group ID(s)
| Attribute | rcsb_polymer_entity_group_membership.group_id |
| Description | A unique identifier for a group of entities |
| Type | string |
| Examples | 1_100 P00003 |
Structure Details
Structure Title
| Attribute | struct.title |
| Description | A title for the data block. The author should attempt to convey the essence of the structure archived in the CIF in the title, and to distinguish this structural result from others. |
| Type | string |
| Examples | T4 lysozyme mutant - S32A Rhinovirus 16 polymerase elongation complex (r1_form) Crystal structure of the OXA-10 W154A mutant at pH 9.0 Mutant structure of Thermus thermophilus HB8 uridine-cytidine kinase Crystal structure of xylanase from Trichoderma longibrachiatum |
Structure Author
| Attribute | audit_author.name |
| Description | The name of an author of this data block. If there are multiple authors, _audit_author.name is looped with _audit_author.address. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). |
| Type | string |
| Examples | Jones, T.J. Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A |
Structure Author ORCID
| Attribute | audit_author.identifier_ORCID |
| Description | The Open Researcher and Contributor ID (ORCID). |
| Type | string |
| Examples | 0000-0002-6681-547X |
Deposit Date
| Attribute | rcsb_accession_info.deposit_date |
| Description | The entry deposition date. |
| Type | string |
| Minimum Value | 1972-08-11 |
| Maximum Value | 2024-12-11 |
| Examples | 2020-07-11 2013-10-01 |
Release Date
| Attribute | rcsb_accession_info.initial_release_date |
| Description | The entry initial release date. |
| Type | string |
| Minimum Value | 1976-05-19 |
| Maximum Value | 2024-12-18 |
| Examples | 2020-01-10 2018-01-23 |
Revision Date
| Attribute | rcsb_accession_info.revision_date |
| Description | The latest entry revision date. |
| Type | string |
| Minimum Value | 2011-07-13 |
| Maximum Value | 2024-12-18 |
| Examples | 2020-02-11 2018-10-23 |
Structural Genomics Project Name
| Attribute | pdbx_SG_project.project_name |
| Description | The value identifies the Structural Genomics project. |
| Type | string |
| Enumeration | Enzyme Function Initiative NIAID, National Institute of Allergy and Infectious Diseases NPPSFA, National Project on Protein Structural and Functional Analyses PSI, Protein Structure Initiative PSI:Biology |
| Examples | PSI, Protein Structure Initiative |
Structural Genomics Project Center Initials
| Attribute | pdbx_SG_project.initial_of_center |
| Description | The value identifies the full name of center. |
| Type | string |
| Enumeration | ATCG3D BIGS BSGC BSGI CEBS CELLMAT CESG CHSAM CHTSB CSBID CSGID CSMP GPCR IFN ISFI ISPC JCSG MCMR MCSG MPID MPP MPSBC MPSbyNMR MSGP MSGPP MTBI NESG NHRs NPCXstals NYCOMPS NYSGRC NYSGXRC NatPro OCSP OPPF PCSEP PSF RSGI S2F SASTAD SECSG SGC SGCGES SGPP SPINE SPINE-2 SSGCID SSPF STEMCELL TBSGC TCELL TEMIMPS TJMP TMPC TransportPDB UC4CDI XMTB YSG |
| Examples | JCSG |
Structural Genomics Project Center Name
| Attribute | pdbx_SG_project.full_name_of_center |
| Description | The value identifies the full name of center. |
| Type | string |
| Enumeration | Accelerated Technologies Center for Gene to 3D Structure Assembly, Dynamics and Evolution of Cell-Cell and Cell-Matrix Adhesions Atoms-to-Animals: The Immune Function Network Bacterial targets at IGS-CNRS, France Berkeley Structural Genomics Center Center for Eukaryotic Structural Genomics Center for High-Throughput Structural Biology Center for Membrane Proteins of Infectious Diseases Center for Structural Biology of Infectious Diseases Center for Structural Genomics of Infectious Diseases Center for Structures of Membrane Proteins Center for the X-ray Structure Determination of Human Transporters Chaperone-Enabled Studies of Epigenetic Regulation Enzymes Enzyme Discovery for Natural Product Biosynthesis GPCR Network Integrated Center for Structure and Function Innovation Israel Structural Proteomics Center Joint Center for Structural Genomics Marseilles Structural Genomics Program @ AFMB Medical Structural Genomics of Pathogenic Protozoa Membrane Protein Structural Biology Consortium Membrane Protein Structures by Solution NMR Midwest Center for Macromolecular Research Midwest Center for Structural Genomics Mitochondrial Protein Partnership Montreal-Kingston Bacterial Structural Genomics Initiative Mycobacterium Tuberculosis Structural Proteomics Project New York Consortium on Membrane Protein Structure New York SGX Research Center for Structural Genomics New York Structural GenomiX Research Consortium New York Structural Genomics Research Consortium Northeast Structural Genomics Consortium Nucleocytoplasmic Transport: a Target for Cellular Control Ontario Centre for Structural Proteomics Oxford Protein Production Facility Paris-Sud Yeast Structural Genomics Partnership for Nuclear Receptor Signaling Code Biology Partnership for Stem Cell Biology Partnership for T-Cell Biology Program for the Characterization of Secreted Effector Proteins Protein Structure Factory RIKEN Structural Genomics/Proteomics Initiative Scottish Structural Proteomics Facility Seattle Structural Genomics Center for Infectious Disease South Africa Structural Targets Annotation Database Southeast Collaboratory for Structural Genomics Structural Genomics Consortium Structural Genomics Consortium for Research on Gene Expression Structural Genomics of Pathogenic Protozoa Consortium Structural Proteomics in Europe Structural Proteomics in Europe 2 Structure 2 Function Project Structure, Dynamics and Activation Mechanisms of Chemokine Receptors Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes Structure-Function Studies of Tight Junction Membrane Proteins Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors TB Structural Genomics Consortium Transcontinental EM Initiative for Membrane Protein Structure Transmembrane Protein Center |
| Examples | Midwest Center for Structural Genomics |
Has Experimental Data
| Attribute | rcsb_accession_info.has_released_experimental_data |
| Description | A code indicating the current availibility of experimental data in the repository. |
| Type | string |
| Enumeration | N Y |
| Examples | Y N |
Compatible with PDB Format
| Attribute | pdbx_database_status.pdb_format_compatible |
| Description | A flag indicating that the entry is compatible with the PDB format. A value of 'N' indicates that the no PDB format data file is corresponding to this entry is available in the PDB archive. |
| Type | string |
| Enumeration | N Y |
| Examples | Y |
Funding Organization
| Attribute | pdbx_audit_support.funding_organization |
| Description | The name of the organization providing funding support for the entry. Funding information is optionally provided for entries after June 2016. |
| Type | string |
| Examples | National Institutes of Health Wellcome Trust National Institutes of Health/National Institute of General Medical Sciences |
Funding Grant Number
| Attribute | pdbx_audit_support.grant_number |
| Description | The grant number associated with this source of support. |
| Type | string |
Funding Country
| Attribute | pdbx_audit_support.country |
| Description | The country/region providing the funding support for the entry. Funding information is optionally provided for entries after June 2016. |
| Type | string |
Content Types Available in the Repository
| Attribute | rcsb_repository_holdings_current.repository_content_types |
| Description | The list of content types associated with this entry. |
| Type | string |
| Enumeration | 2fo-fc Map Combined NMR data (NEF) Combined NMR data (NMR-STAR) FASTA sequence Map Coefficients NMR chemical shifts NMR restraints V1 NMR restraints V2 assembly PDB assembly mmCIF entry PDB entry PDB bundle entry PDBML entry mmCIF fo-fc Map structure factors validation 2fo-fc coefficients validation data mmCIF validation fo-fc coefficients validation report validation slider image |
| Examples | entry mmCIF |
Content Types Available in a Related Resource
| Attribute | pdbx_database_related.content_type |
| Description | The identifying content type of the related entry. |
| Type | string |
| Enumeration | associated EM volume associated NMR restraints associated SAS data associated structure factors complete structure consensus EM volume derivative structure ensemble focused EM volume minimized average structure native structure other other EM volume protein target sequence and/or protocol data re-refinement representative structure split unspecified |
| Examples | minimized average structure representative structure ensemble derivative structure native structure associated EM volume other EM volume associated NMR restraints associated structure factors associated SAS data protein target sequence and/or protocol data split re-refinement complete structure unspecified other |
Related Resource Name Containing Additional Content
| Attribute | pdbx_database_related.db_name |
| Description | The name of the database containing the related entry. |
| Type | string |
| Enumeration | BIOISIS BMCD BMRB EMDB NDB PDB PDB-Dev SASBDB TargetDB TargetTrack |
| Examples | PDB - Protein Databank
NDB - Nucleic Acid Database
BMRB - BioMagResBank
EMDB - Electron Microscopy Database
BMCD - Biological Macromolecule Crystallization Database
TargetTrack - Target Registration and Protocol Database
SASBDB - Small Angle Scattering Biological Data Bank |
Structure Determination Methodology
| Attribute | rcsb_entry_info.structure_determination_methodology |
| Description | Indicates if the structure was determined using experimental or computational methods. |
| Type | string |
| Enumeration | computational experimental |
| Examples | experimental |
Computed Structure Model Details
Computed Structure Model ID(s)
| Attribute | rcsb_comp_model_provenance.entry_id |
| Description | Entry identifier corresponding to the computed structure model. |
| Type | string |
| Examples | AF-P60325-F1 ma-bak-cepc-0019 |
Source Database
| Attribute | rcsb_comp_model_provenance.source_db |
| Description | Source database for the computed structure model. |
| Type | string |
| Enumeration | AlphaFoldDB ModelArchive |
Global Quality Score - pLDDT
| Attribute | rcsb_ma_qa_metric_global.ma_qa_metric_global.value |
| Description | Value of the global QA metric. |
| Type | number |
| Nested Attribute | rcsb_ma_qa_metric_global.ma_qa_metric_global.type |
| Nested Attribute Minimum Value | 23.15 |
| Nested Attribute Maximum Value | 98.77 |
| Nested Attribute Examples | 83.02 29.14 |
Entry Features
Entry Polymer Types
| Attribute | rcsb_entry_info.selected_polymer_entity_types |
| Description | Selected polymer entity type categories describing the entry. |
| Type | string |
| Enumeration | Nucleic acid (only) Oligosaccharide (only) Other Protein (only) Protein/NA Protein/Oligosaccharide |
| Examples | Protein (only) |
Entry Polymer Composition
| Attribute | rcsb_entry_info.polymer_composition |
| Description | Categories describing the polymer entity composition for the entry. |
| Type | string |
| Enumeration | DNA DNA/RNA NA-hybrid NA/oligosaccharide RNA heteromeric protein homomeric protein oligosaccharide other other type composition other type pair protein/NA protein/NA/oligosaccharide protein/oligosaccharide |
| Examples | homomeric protein |
Molecular Weight per Deposited Model
| Attribute | rcsb_entry_info.molecular_weight |
| Description | The molecular mass (KDa) of polymer and non-polymer entities (exclusive of solvent) in the deposited structure entry. |
| Type | number |
| Minimum Value | 0.42 |
| Maximum Value | 63486.35 |
| Examples | 33.43 45.53 |
Number of Assemblies
| Attribute | rcsb_entry_info.assembly_count |
| Description | The number of assemblies defined for this entry including the deposited assembly. |
| Type | integer |
| Minimum Value | 1 |
| Maximum Value | 44 |
Number of Distinct Molecular Entities
| Attribute | rcsb_entry_info.entity_count |
| Description | The number of distinct polymer, non-polymer, branched molecular, and solvent entities per deposited structure model. |
| Type | integer |
| Minimum Value | 1 |
| Maximum Value | 455 |
Number of Distinct Non-polymer Entities
| Attribute | rcsb_entry_info.nonpolymer_entity_count |
| Description | The number of distinct non-polymer entities in the structure entry exclusive of solvent. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 30 |
Number of Distinct Protein Entities
| Attribute | rcsb_entry_info.polymer_entity_count_protein |
| Description | The number of distinct protein polymer entities. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 150 |
Number of Distinct RNA Entities
| Attribute | rcsb_entry_info.polymer_entity_count_RNA |
| Description | The number of distinct RNA polymer entities. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 36 |
Number of Distinct DNA Entities
| Attribute | rcsb_entry_info.polymer_entity_count_DNA |
| Description | The number of distinct DNA polymer entities. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 455 |
Number of Distinct NA Hybrid Entities
| Attribute | rcsb_entry_info.polymer_entity_count_nucleic_acid_hybrid |
| Description | The number of distinct hybrid nucleic acid polymer entities. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 3 |
Total Number of Polymer Instances (Chains)
| Attribute | rcsb_entry_info.deposited_polymer_entity_instance_count |
| Description | The number of polymer instances in the deposited data set. This is the total count of polymer entity instances reported per deposited structure model. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 1792 |
Total Number of Non-polymer Instances
| Attribute | rcsb_entry_info.deposited_nonpolymer_entity_instance_count |
| Description | The number of non-polymer instances in the deposited data set. This is the total count of non-polymer entity instances reported per deposited structure model. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 5351 |
Total Number of Polymer Residues per Deposited Model
| Attribute | rcsb_entry_info.deposited_polymer_monomer_count |
| Description | The number of polymer monomers in sample entity instances in the deposited data set. This is the total count of monomers for all polymer entity instances reported per deposited structure model. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 566853 |
Number of Non-Hydrogen Atoms per Deposited Model
| Attribute | rcsb_entry_info.deposited_atom_count |
| Description | The number of heavy atom coordinates records per deposited structure model. |
| Type | integer |
| Minimum Value | 28 |
| Maximum Value | 3968189 |
Number of Hydrogen Atoms per Deposited Model
| Attribute | rcsb_entry_info.deposited_hydrogen_atom_count |
| Description | The number of hydrogen atom coordinates records per deposited structure model. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 680778 |
Number of Water Molecules per Deposited Model
| Attribute | rcsb_entry_info.deposited_solvent_atom_count |
| Description | The number of heavy solvent atom coordinates records per deposited structure model. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 17738 |
Number of Deuterated Water Molecules per Deposited Model
| Attribute | rcsb_entry_info.deposited_deuterated_water_count |
| Description | The number of deuterated water molecules per deposited structure model. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 1114 |
Deposited Model Count
| Attribute | rcsb_entry_info.deposited_model_count |
| Description | The number of model structures deposited. |
| Type | integer |
| Minimum Value | 1 |
| Maximum Value | 640 |
Disulfide Bond Count per Deposited Model
| Attribute | rcsb_entry_info.disulfide_bond_count |
| Description | The number of disulfide bonds per deposited structure model. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 1356 |
Polymer Molecular Features
Polymer Entity Description
| Attribute | rcsb_polymer_entity.pdbx_description |
| Description | A description of the polymer entity. |
| Type | string |
| Examples | Green fluorescent protein 23S ribosomal RNA NAD-dependent protein deacylase sirtuin-5, mitochondrial |
Macromolecule Name
| Attribute | rcsb_polymer_entity.rcsb_macromolecular_names_combined.name |
| Description | Combined list of macromolecular names. |
| Type | string |
| Examples | Lysozyme C Plasmid recombination enzyme Pyruvate carboxylase |
Polymer Entity Type
| Attribute | entity_poly.rcsb_entity_polymer_type |
| Description | A coarse-grained polymer entity type. |
| Type | string |
| Enumeration | Protein DNA RNA NA-hybrid Other |
Polymer Entity Sequence Length
| Attribute | entity_poly.rcsb_sample_sequence_length |
| Description | The monomer length of the sample sequence. |
| Type | integer |
| Minimum Value | 1 |
| Maximum Value | 19000 |
Polymer Entity Mutation Count
| Attribute | entity_poly.rcsb_mutation_count |
| Description | Number of engineered mutations engineered in the sample sequence. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 657 |
Polymer Entity Molecular Weight
| Attribute | rcsb_polymer_entity.formula_weight |
| Description | Formula mass (KDa) of the entity. |
| Type | number |
| Minimum Value | 0.16 |
| Maximum Value | 6061.92 |
| Examples | 40 105 |
Glycosylation Site
| Attribute | rcsb_polymer_struct_conn.role |
| Description | The chemical or structural role of the interaction |
| Type | string |
| Enumeration | C-Mannosylation N-Glycosylation O-Glycosylation S-Glycosylation |
| Examples | N-Glycosylation O-Glycosylation |
Gene Name
| Attribute | rcsb_entity_source_organism.rcsb_gene_name.value |
| Description | Gene name. |
| Type | string |
| Examples | lacA hemH |
Source Organism Taxonomy Name (Full Lineage)
| Attribute | rcsb_entity_source_organism.taxonomy_lineage.name |
| Description | Memebers of the NCBI Taxonomy lineage as parent taxonomy names. |
| Type | string |
| Examples | Homo sapiens Mus musculus |
Polymer Entity Name Combined
| Attribute | rcsb_polymer_entity.rcsb_polymer_name_combined.names |
| Description | Protein name annotated by the UniProtKB or macromolecular name assigned by the PDB |
| Type | string |
Source Organism Taxonomy ID (Full Lineage)
| Attribute | rcsb_entity_source_organism.taxonomy_lineage.id |
| Description | Members of the NCBI Taxonomy lineage as parent taxonomy idcodes. |
| Type | string |
| Examples | 9606 10090 |
Scientific Name of the Source Organism
| Attribute | rcsb_entity_source_organism.ncbi_scientific_name |
| Description | The scientific name associated with this taxonomy code aggregated by the NCBI Taxonomy Database. This name corresponds to the taxonomy identifier assigned by the PDB depositor. References: Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009). GenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31. Epub 2008 Oct 21. |
| Type | string |
Parent Scientific Name (typically superkingdom or clade)
| Attribute | rcsb_entity_source_organism.ncbi_parent_scientific_name |
| Description | A parent scientific name in the NCBI taxonomy hierarchy of the source organism assigned by the PDB depositor. For cellular organism this corresponds to a superkingdom (e.g., Archaea, Bacteria, Eukaryota). For viruses this corresponds to a clade (e.g. Adnaviria, Bicaudaviridae, Clavaviridae). For other and unclassified entries this corresponds to the first level of any taxonomic rank below the root level. References: Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009). GenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31. Epub 2008 Oct 21. |
| Type | string |
| Examples | Archaea Bacteria Eukaryota Adnaviria Bicaudaviridae Clavaviridae Duplodnaviria |
Source Organism Type
| Attribute | rcsb_entity_source_organism.source_type |
| Description | The source type for the entity |
| Type | string |
| Enumeration | genetically engineered natural synthetic |
Polymer Entity Source Count
| Attribute | rcsb_polymer_entity.rcsb_source_part_count |
| Description | The number of biological sources for the polymer entity. Multiple source contributions may come from the same organism (taxonomy). |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 21 |
Polymer Entity Distinct Taxonomy Count
| Attribute | rcsb_polymer_entity.rcsb_source_taxonomy_count |
| Description | The number of distinct source taxonomies for the polymer entity. Commonly used to identify chimeric polymers. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 5 |
Expression System Organism Taxonomy Name
| Attribute | rcsb_entity_host_organism.taxonomy_lineage.name |
| Description | Members of the NCBI Taxonomy lineage as parent taxonomy names. |
| Type | string |
| Examples | Escherichia coli BL21(DE3) Baculovirus |
Expression System Organism Taxonomy ID
| Attribute | rcsb_entity_host_organism.taxonomy_lineage.id |
| Description | Members of the NCBI Taxonomy lineage as parent taxonomy idcodes. |
| Type | string |
| Examples | 469008 10469 |
Enzyme Classification Number
| Attribute | rcsb_polymer_entity.rcsb_ec_lineage.id |
| Description | Members of the enzyme classification lineage as parent classification codes. |
| Type | string |
| Examples | 2 2.7.1.153 |
| Iterable | true |
Enzyme Classification Name
| Attribute | rcsb_polymer_entity.rcsb_ec_lineage.name |
| Description | Members of the enzyme classification lineage as parent classification names. |
| Type | string |
| Examples | Transferases phosphatidylinositol-4,5-bisphosphate 3-kinase |
Identifier - Pfam Protein Family
| Attribute | rcsb_polymer_entity_annotation.annotation_id |
| Description | An identifier for the annotation. |
| Type | string |
| Nested Attribute | rcsb_polymer_entity_annotation.type |
| Nested Attribute Examples | PF00049 PF00441 |
Name - Pfam Protein Family
| Attribute | rcsb_polymer_entity_annotation.name |
| Description | A name for the annotation. |
| Type | string |
| Nested Attribute | rcsb_polymer_entity_annotation.type |
| Nested Attribute Examples | Insulin/IGF/Relaxin family (Insulin) Acyl-CoA dehydrogenase, C-terminal domain (Acyl-CoA_dh_1) |
Name - IMPC Phenotype
| Attribute | rcsb_uniprot_annotation.name |
| Description | A name for the annotation. |
| Type | string |
| Nested Attribute | rcsb_uniprot_annotation.type |
| Nested Attribute Examples | immune system phenotype mortality/aging |
Lineage Identifier - CARD
| Attribute | rcsb_polymer_entity_annotation.annotation_lineage.id |
| Description | Members of the annotation lineage as parent class identifiers. |
| Type | string |
| Nested Attribute | rcsb_polymer_entity_annotation.type |
| Nested Attribute Examples | ARO:3001059 ARO:3000015 |
Lineage Identifier - Membrane Proteins of Known 3D Structure
| Attribute | rcsb_polymer_entity_annotation.annotation_lineage.id |
| Description | Members of the annotation lineage as parent class identifiers. |
| Type | string |
| Nested Attribute | rcsb_polymer_entity_annotation.type |
| Nested Attribute Examples | MONOTOPIC MEMBRANE PROTEINS.Oxidases.Monoamine Oxidase A |
Lineage Identifier - Orientations of Proteins in Membranes (OPM) Database
| Attribute | rcsb_polymer_entity_annotation.annotation_lineage.id |
| Description | Members of the annotation lineage as parent class identifiers. |
| Type | string |
| Nested Attribute | rcsb_polymer_entity_annotation.type |
| Nested Attribute Examples | Transmembrane.Bitopic proteins.Bitopic proteins with NAD(P)-binding Rossmann-fold domains.Flavin containing amine oxidoreductase |
Chromosomal Locus (Browser ID)
| Attribute | rcsb_genomic_lineage.id |
| Description | Automatically assigned ID that uniquely identifies taxonomy, chromosome or gene in the Genome Location Browser. |
| Type | string |
| Examples | 9606 568815441 414325 |
Lineage Identifier - Pharos Disease
| Attribute | rcsb_uniprot_annotation.annotation_lineage.id |
| Description | Members of the annotation lineage as parent class identifiers. |
| Type | string |
| Nested Attribute | rcsb_uniprot_annotation.type |
| Nested Attribute Examples | MONDO:0100118 MONDO:0002051 |
Lineage Identifier - Gene Ontology
| Attribute | rcsb_uniprot_annotation.annotation_lineage.id |
| Description | Members of the annotation lineage as parent class identifiers. |
| Type | string |
| Nested Attribute | rcsb_uniprot_annotation.type |
| Nested Attribute Examples | GO:0005575 GO:0005622 |
Lineage Identifier - InterPro Protein Family
| Attribute | rcsb_uniprot_annotation.annotation_lineage.id |
| Description | Members of the annotation lineage as parent class identifiers. |
| Type | string |
| Nested Attribute | rcsb_uniprot_annotation.type |
| Nested Attribute Examples | IPR022352 IPR004825 |
Lineage Name - CARD
| Attribute | rcsb_polymer_entity_annotation.annotation_lineage.name |
| Description | Members of the annotation lineage as parent class names. |
| Type | string |
| Nested Attribute | rcsb_polymer_entity_annotation.type |
| Nested Attribute Examples | SHV-1 SHV beta-lactamase |
Lineage Name - Membrane Proteins of Known 3D Structure
| Attribute | rcsb_polymer_entity_annotation.annotation_lineage.name |
| Description | Members of the annotation lineage as parent class names. |
| Type | string |
| Nested Attribute | rcsb_polymer_entity_annotation.type |
| Nested Attribute Examples | Monoamine Oxidase A |
Lineage Name - Orientations of Proteins in Membranes (OPM) Database
| Attribute | rcsb_polymer_entity_annotation.annotation_lineage.name |
| Description | Members of the annotation lineage as parent class names. |
| Type | string |
| Nested Attribute | rcsb_polymer_entity_annotation.type |
| Nested Attribute Examples | Flavin containing amine oxidoreductase |
Lineage Name - Pharos Disease
| Attribute | rcsb_uniprot_annotation.annotation_lineage.name |
| Description | Members of the annotation lineage as parent class names. |
| Type | string |
| Nested Attribute | rcsb_uniprot_annotation.type |
| Nested Attribute Examples | hepatocellular carcinoma tuberculosis |
Lineage Name - Gene Ontology
| Attribute | rcsb_uniprot_annotation.annotation_lineage.name |
| Description | Members of the annotation lineage as parent class names. |
| Type | string |
| Nested Attribute | rcsb_uniprot_annotation.type |
| Nested Attribute Examples | cellular_component intracellular |
Lineage Name - InterPro Protein Family
| Attribute | rcsb_uniprot_annotation.annotation_lineage.name |
| Description | Members of the annotation lineage as parent class names. |
| Type | string |
| Nested Attribute | rcsb_uniprot_annotation.type |
| Nested Attribute Examples | Insulin family Insulin |
Count Per Polymer Entity - Cloning artifact, expression tag, linker
| Attribute | rcsb_polymer_entity_feature_summary.count |
| Description | The feature count. |
| Type | integer |
| Nested Attribute | rcsb_polymer_entity_feature_summary.type |
| Nested Attribute Minimum Value | 1 |
| Nested Attribute Maximum Value | 22 |
| Nested Attribute Examples | 1 10 |
Count Per Polymer Entity - Modified chemical component
| Attribute | rcsb_polymer_entity_feature_summary.count |
| Description | The feature count. |
| Type | integer |
| Nested Attribute | rcsb_polymer_entity_feature_summary.type |
| Nested Attribute Minimum Value | 1 |
| Nested Attribute Maximum Value | 4128 |
| Nested Attribute Examples | 2 5 |
Coverage Fraction Per Polymer Entity - Cloning artifact, expression tag, linker
| Attribute | rcsb_polymer_entity_feature_summary.coverage |
| Description | The fractional feature coverage relative to the full entity sequence. For instance, the fraction of features such as mutations, artifacts or modified monomers relative to the length of the entity sequence. |
| Type | number |
| Nested Attribute | rcsb_polymer_entity_feature_summary.type |
| Nested Attribute Examples | 0.02 0.12 |
Coverage Fraction Per Polymer Entity - Modified chemical component
| Attribute | rcsb_polymer_entity_feature_summary.coverage |
| Description | The fractional feature coverage relative to the full entity sequence. For instance, the fraction of features such as mutations, artifacts or modified monomers relative to the length of the entity sequence. |
| Type | number |
| Nested Attribute | rcsb_polymer_entity_feature_summary.type |
| Nested Attribute Examples | 0.01 0.05 |
Reference Sequence Coverage - UniProt
| Attribute | rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.reference_sequence_coverage |
| Description | Indicates what fraction of the reference sequence is covered by this polymer entity sequence. |
| Type | number |
| Nested Attribute | rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_name |
| Nested Attribute Examples | 0.25 0.75 |
Entity Sequence Coverage - UniProt
| Attribute | rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.entity_sequence_coverage |
| Description | Indicates what fraction of this polymer entity sequence is covered by the reference sequence. |
| Type | number |
| Nested Attribute | rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_name |
| Nested Attribute Examples | 0.25 0.75 |
Polymer Instance (Chain) Features
Lineage Identifier - CATH
| Attribute | rcsb_polymer_instance_annotation.annotation_lineage.id |
| Description | Members of the annotation lineage as parent class identifiers. |
| Type | string |
| Nested Attribute | rcsb_polymer_instance_annotation.type |
| Nested Attribute Examples | 2.30.30.40 3.30.420.40 |
Lineage Identifier - SCOP
| Attribute | rcsb_polymer_instance_annotation.annotation_lineage.id |
| Description | Members of the annotation lineage as parent class identifiers. |
| Type | string |
| Nested Attribute | rcsb_polymer_instance_annotation.type |
| Nested Attribute Examples | 82057 53067 |
Lineage Identifier - SCOP2 Family/Superfamily
| Attribute | rcsb_polymer_instance_annotation.annotation_lineage.id |
| Description | Members of the annotation lineage as parent class identifiers. |
| Type | string |
| Nested Attribute | rcsb_polymer_instance_annotation.type |
| Nested Attribute Examples | 3001607 4000551 2000122 1000001 |
Lineage Identifier - ECOD
| Attribute | rcsb_polymer_instance_annotation.annotation_lineage.id |
| Description | Members of the annotation lineage as parent class identifiers. |
| Type | string |
| Nested Attribute | rcsb_polymer_instance_annotation.type |
| Nested Attribute Examples | 100001 300013 |
Lineage Name - CATH
| Attribute | rcsb_polymer_instance_annotation.annotation_lineage.name |
| Description | Members of the annotation lineage as parent class names. |
| Type | string |
| Nested Attribute | rcsb_polymer_instance_annotation.type |
| Nested Attribute Examples | SH3 Domains ATP Synthase |
Lineage Name - SCOP
| Attribute | rcsb_polymer_instance_annotation.annotation_lineage.name |
| Description | Members of the annotation lineage as parent class names. |
| Type | string |
| Nested Attribute | rcsb_polymer_instance_annotation.type |
| Nested Attribute Examples | Prokaryotic SH3-related domain Actin-like ATPase domain |
Lineage Name - SCOP2 Family/Superfamily
| Attribute | rcsb_polymer_instance_annotation.annotation_lineage.name |
| Description | Members of the annotation lineage as parent class names. |
| Type | string |
| Nested Attribute | rcsb_polymer_instance_annotation.type |
| Nested Attribute Examples | Sialidases (neuraminidases) FAD-dependent thiol oxidase Globin-like Sialidases |
Lineage Name - ECOD
| Attribute | rcsb_polymer_instance_annotation.annotation_lineage.name |
| Description | Members of the annotation lineage as parent class names. |
| Type | string |
| Nested Attribute | rcsb_polymer_instance_annotation.type |
| Nested Attribute Examples | F: Evr1_Alr F: Peptidase_C30_C |
Count Per Polymer Chain - CIS Peptide linkages
| Attribute | rcsb_polymer_instance_feature_summary.count |
| Description | The feature count per polymer chain. |
| Type | integer |
| Nested Attribute | rcsb_polymer_instance_feature_summary.type |
| Nested Attribute Minimum Value | 1 |
| Nested Attribute Maximum Value | 301 |
| Nested Attribute Examples | 1 10 |
Count Per Polymer Chain - Protein helices
| Attribute | rcsb_polymer_instance_feature_summary.count |
| Description | The feature count per polymer chain. |
| Type | integer |
| Nested Attribute | rcsb_polymer_instance_feature_summary.type |
| Nested Attribute Minimum Value | 1 |
| Nested Attribute Maximum Value | 374 |
| Nested Attribute Examples | 1 10 |
Count Per Polymer Chain - Beta-sheets
| Attribute | rcsb_polymer_instance_feature_summary.count |
| Description | The feature count per polymer chain. |
| Type | integer |
| Nested Attribute | rcsb_polymer_instance_feature_summary.type |
| Nested Attribute Minimum Value | 1 |
| Nested Attribute Maximum Value | 289 |
| Nested Attribute Examples | 1 10 |
Count Per Polymer Chain - Real space density correlation outlier
| Attribute | rcsb_polymer_instance_feature_summary.count |
| Description | The feature count per polymer chain. |
| Type | integer |
| Nested Attribute | rcsb_polymer_instance_feature_summary.type |
| Nested Attribute Minimum Value | 1 |
| Nested Attribute Maximum Value | 2824 |
| Nested Attribute Examples | 1 10 |
Count Per Polymer Chain - Real space outlier
| Attribute | rcsb_polymer_instance_feature_summary.count |
| Description | The feature count per polymer chain. |
| Type | integer |
| Nested Attribute | rcsb_polymer_instance_feature_summary.type |
| Nested Attribute Minimum Value | 1 |
| Nested Attribute Maximum Value | 2825 |
| Nested Attribute Examples | 1 10 |
Coverage Fraction Per Polymer Chain - Protein helices
| Attribute | rcsb_polymer_instance_feature_summary.coverage |
| Description | The fractional feature coverage relative to the full entity sequence. For instance, the fraction of features such as CATH or SCOP domains, secondary structure elements, unobserved residues, or geometrical outliers relative to the length of the entity sequence. |
| Type | number |
| Nested Attribute | rcsb_polymer_instance_feature_summary.type |
| Nested Attribute Examples | 0.15 0.45 |
Coverage Fraction Per Polymer Chain - Beta-sheets
| Attribute | rcsb_polymer_instance_feature_summary.coverage |
| Description | The fractional feature coverage relative to the full entity sequence. For instance, the fraction of features such as CATH or SCOP domains, secondary structure elements, unobserved residues, or geometrical outliers relative to the length of the entity sequence. |
| Type | number |
| Nested Attribute | rcsb_polymer_instance_feature_summary.type |
| Nested Attribute Examples | 0.15 0.45 |
Coverage Fraction Per Polymer Chain - Unobserved Residues
| Attribute | rcsb_polymer_instance_feature_summary.coverage |
| Description | The fractional feature coverage relative to the full entity sequence. For instance, the fraction of features such as CATH or SCOP domains, secondary structure elements, unobserved residues, or geometrical outliers relative to the length of the entity sequence. |
| Type | number |
| Nested Attribute | rcsb_polymer_instance_feature_summary.type |
| Nested Attribute Examples | 0.15 0.45 |
Coverage Fraction Per Polymer Chain - Unobserved Atoms
| Attribute | rcsb_polymer_instance_feature_summary.coverage |
| Description | The fractional feature coverage relative to the full entity sequence. For instance, the fraction of features such as CATH or SCOP domains, secondary structure elements, unobserved residues, or geometrical outliers relative to the length of the entity sequence. |
| Type | number |
| Nested Attribute | rcsb_polymer_instance_feature_summary.type |
| Nested Attribute Examples | 0.15 0.45 |
Nonpolymer Molecular Features
Component Identifier
| Attribute | rcsb_nonpolymer_entity_container_identifiers.nonpolymer_comp_id |
| Description | Non-polymer(ligand) chemical component identifier for the entity in this container. |
| Type | string |
| Examples | GTP STN |
Component Identifier - Investigated Molecule
| Attribute | rcsb_nonpolymer_entity_annotation.comp_id |
| Description | Non-polymer(ligand) chemical component identifier for the entity. |
| Type | string |
| Nested Attribute | rcsb_nonpolymer_entity_annotation.type |
| Nested Attribute Examples | BEZ PQM |
Component Identifier - Has Covalent Linkage
| Attribute | rcsb_nonpolymer_instance_annotation.comp_id |
| Description | Non-polymer (ligand) chemical component identifier. |
| Type | string |
| Nested Attribute | rcsb_nonpolymer_instance_annotation.type |
| Nested Attribute Examples | BMZ ATP |
Component Identifier - Has Metal Coordination
| Attribute | rcsb_nonpolymer_instance_annotation.comp_id |
| Description | Non-polymer (ligand) chemical component identifier. |
| Type | string |
| Nested Attribute | rcsb_nonpolymer_instance_annotation.type |
| Nested Attribute Examples | SF4 HEM |
Component Identifier - Has No Covalent Linkage
| Attribute | rcsb_nonpolymer_instance_annotation.comp_id |
| Description | Non-polymer (ligand) chemical component identifier. |
| Type | string |
| Nested Attribute | rcsb_nonpolymer_instance_annotation.type |
| Nested Attribute Examples | J5C DID |
Binding Affinity Value - IC50
| Attribute | rcsb_binding_affinity.value |
| Description | Binding affinity value between a ligand and its target molecule. |
| Type | number |
| Nested Attribute | rcsb_binding_affinity.type |
| Nested Attribute Minimum Value | 0.0 |
| Nested Attribute Maximum Value | 8.0e8 |
| Nested Attribute Examples | 0.8 14 |
| Units | nM |
Binding Affinity Value - EC50
| Attribute | rcsb_binding_affinity.value |
| Description | Binding affinity value between a ligand and its target molecule. |
| Type | number |
| Nested Attribute | rcsb_binding_affinity.type |
| Nested Attribute Minimum Value | 0.0040 |
| Nested Attribute Maximum Value | 5.0e7 |
| Nested Attribute Examples | 0.18 23000 |
| Units | nM |
Binding Affinity Value - Kd
| Attribute | rcsb_binding_affinity.value |
| Description | Binding affinity value between a ligand and its target molecule. |
| Type | number |
| Nested Attribute | rcsb_binding_affinity.type |
| Nested Attribute Minimum Value | 0.0 |
| Nested Attribute Maximum Value | 2.5e8 |
| Nested Attribute Examples | 6.5 220000 |
| Units | nM |
Binding Affinity Value - Ka
| Attribute | rcsb_binding_affinity.value |
| Description | Binding affinity value between a ligand and its target molecule. |
| Type | number |
| Nested Attribute | rcsb_binding_affinity.type |
| Nested Attribute Examples | 7.5 1700 |
| Units | M⁻¹ |
Binding Affinity Value - Ki
| Attribute | rcsb_binding_affinity.value |
| Description | Binding affinity value between a ligand and its target molecule. |
| Type | number |
| Nested Attribute | rcsb_binding_affinity.type |
| Nested Attribute Minimum Value | 0.0 |
| Nested Attribute Maximum Value | 4.0e8 |
| Nested Attribute Examples | 4 390000 |
| Units | nM |
Binding Affinity Value - ΔG
| Attribute | rcsb_binding_affinity.value |
| Description | Binding affinity value between a ligand and its target molecule. |
| Type | number |
| Nested Attribute | rcsb_binding_affinity.type |
| Nested Attribute Minimum Value | -65 |
| Nested Attribute Maximum Value | 30 |
| Nested Attribute Examples | 17.2 21.4 |
| Units | kJ/mol |
Binding Affinity Value - ΔH
| Attribute | rcsb_binding_affinity.value |
| Description | Binding affinity value between a ligand and its target molecule. |
| Type | number |
| Nested Attribute | rcsb_binding_affinity.type |
| Nested Attribute Minimum Value | -1.3e2 |
| Nested Attribute Maximum Value | 73 |
| Nested Attribute Examples | 66.9 123 |
| Units | kJ/mol |
Binding Affinity Value - -TΔS
| Attribute | rcsb_binding_affinity.value |
| Description | Binding affinity value between a ligand and its target molecule. |
| Type | number |
| Nested Attribute | rcsb_binding_affinity.type |
| Nested Attribute Minimum Value | -1.0e2 |
| Nested Attribute Maximum Value | 1.7e3 |
| Nested Attribute Examples | 18.1 47.2 |
| Units | kJ/mol |
Oligosaccharide/Branched Molecular Features
Branched Entity Type
| Attribute | pdbx_entity_branch.type |
| Description | The type of this branched oligosaccharide. |
| Type | string |
| Enumeration | oligosaccharide |
Oligosaccharide Entity Description
| Attribute | rcsb_branched_entity.pdbx_description |
| Description | A description of the branched entity. |
| Type | string |
| Examples | alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose beta-D-xylopyranose-(1-4)-beta-D-xylopyranose |
Oligosaccharide Formula Weight
| Attribute | rcsb_branched_entity.formula_weight |
| Description | Formula mass (KDa) of the branched entity. |
| Type | number |
| Minimum Value | 0.27 |
| Maximum Value | 10.41 |
| Examples | 0.745 1.2 |
Oligosaccharide Linear Descriptor - LINUCS
| Attribute | pdbx_entity_branch_descriptor.descriptor |
| Description | This data item contains the descriptor value for this entity. |
| Type | string |
| Nested Attribute | pdbx_entity_branch_descriptor.type |
| Nested Attribute Examples | [][a-D-Manp]{[(2+1)][a-D-Manp]{}} []{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}} |
Oligosaccharide Linear Descriptor - Glycam Condensed Sequence
| Attribute | pdbx_entity_branch_descriptor.descriptor |
| Description | This data item contains the descriptor value for this entity. |
| Type | string |
| Nested Attribute | pdbx_entity_branch_descriptor.type |
| Nested Attribute Examples | DManpa1-2DManpa1-ROH DManpb1-4DGlcpNAcb1-4DGlcpNAcb1- |
Oligosaccharide Linear Descriptor - WURCS
| Attribute | pdbx_entity_branch_descriptor.descriptor |
| Description | This data item contains the descriptor value for this entity. |
| Type | string |
| Nested Attribute | pdbx_entity_branch_descriptor.type |
| Nested Attribute Examples | WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1 WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1 |
Oligosaccharide Component Count
| Attribute | pdbx_entity_branch.rcsb_branched_component_count |
| Description | Number of constituent chemical components in the branched entity. |
| Type | integer |
| Minimum Value | 2 |
| Maximum Value | 36 |
Oligosaccharide Component List
| Attribute | rcsb_branched_entity_container_identifiers.chem_comp_monomers |
| Description | Unique list of monomer chemical component identifiers in the entity in this container. |
| Type | string |
| Examples | NAG MAN GAL |
| Iterable | true |
Assembly Features
Number of Non-Hydrogen Atoms per Assembly
| Attribute | rcsb_assembly_info.atom_count |
| Description | The assembly non-hydrogen atomic coordinate count. |
| Type | integer |
| Minimum Value | 7 |
| Maximum Value | 39959280 |
Number of Hydrogen Atoms per Assembly
| Attribute | rcsb_assembly_info.hydrogen_atom_count |
| Description | The assembly hydrogen atomic coordinate count. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 5795340 |
Number of Water Molecules per Assembly
| Attribute | rcsb_assembly_info.solvent_atom_count |
| Description | The assembly non-hydrogen solvent atomic coordinate count. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 78540 |
Number of Deuterated Water Molecules per Assembly
| Attribute | rcsb_assembly_info.deuterated_water_count |
| Description | The assembly deuterated water molecule count. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 2228 |
Number of Polymer Residues per Assembly
| Attribute | rcsb_assembly_info.polymer_monomer_count |
| Description | The number of polymer monomers in sample entity instances comprising the assembly data set. This is the total count of monomers for all polymer entity instances in the generated assembly coordinate data. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 5340600 |
Number of Modeled Polymer Residues per Assembly
| Attribute | rcsb_assembly_info.modeled_polymer_monomer_count |
| Description | The number of modeled polymer monomers in the assembly coordinate data. This is the total count of monomers with reported coordinate data for all polymer entity instances in the generated assembly coordinate data. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 5086680 |
Number of Unmodeled Polymer Residues per Assembly
| Attribute | rcsb_assembly_info.unmodeled_polymer_monomer_count |
| Description | The number of unmodeled polymer monomers in the assembly coordinate data. This is the total count of monomers with unreported coordinate data for all polymer entity instances in the generated assembly coordinate data. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 515880 |
Number of Polymer Instances (Chains) per Assembly
| Attribute | rcsb_assembly_info.polymer_entity_instance_count |
| Description | The number of polymer instances in the generated assembly data set. This is the total count of polymer entity instances generated in the assembly coordinate data. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 8280 |
Number of Non-polymer Instances per Assembly
| Attribute | rcsb_assembly_info.nonpolymer_entity_instance_count |
| Description | The number of non-polymer instances in the generated assembly data set exclusive of solvent. This is the total count of non-polymer entity instances generated in the assembly coordinate data. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 4593 |
Number of Protein Instances (Chains) per Assembly
| Attribute | rcsb_assembly_info.polymer_entity_instance_count_protein |
| Description | The number of protein polymer instances in the generated assembly data set. This is the total count of protein polymer entity instances generated in the assembly coordinate data. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 8280 |
Number of DNA Instances (Chains) per Assembly
| Attribute | rcsb_assembly_info.polymer_entity_instance_count_DNA |
| Description | The number of DNA polymer instances in the generated assembly data set. This is the total count of DNA polymer entity instances generated in the assembly coordinate data. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 455 |
Number of RNA Instances (Chains) per Assembly
| Attribute | rcsb_assembly_info.polymer_entity_instance_count_RNA |
| Description | The number of RNA polymer instances in the generated assembly data set. This is the total count of RNA polymer entity instances generated in the assembly coordinate data. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 180 |
Number of NA Hybrid Instances (Chains) per Assembly
| Attribute | rcsb_assembly_info.polymer_entity_instance_count_nucleic_acid_hybrid |
| Description | The number of hybrid nucleic acide polymer instances in the generated assembly data set. This is the total count of hybrid nucleic acid polymer entity instances generated in the assembly coordinate data. |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 8 |
Assembly Experimental Support
| Attribute | pdbx_struct_assembly_auth_evidence.experimental_support |
| Description | Provides the experimental method to determine the state of this assembly |
| Type | string |
| Enumeration | NMR Distance Restraints NMR relaxation study SAXS assay for oligomerization cross-linking electron microscopy equilibrium centrifugation fluorescence resonance energy transfer gel filtration homology immunoprecipitation isothermal titration calorimetry light scattering mass spectrometry microscopy native gel electrophoresis none scanning transmission electron microscopy surface plasmon resonance |
Assembly Experimental Support Details
| Attribute | pdbx_struct_assembly_auth_evidence.details |
| Description | Provides any additional information regarding the evidence of this assembly |
| Type | string |
| Examples | Homology to bacteriorhodopsin Helical filament was observed by negative staining and Cryo-EM |
Symmetry Symbol
| Attribute | rcsb_struct_symmetry.symbol |
| Description | Symmetry symbol refers to point group or helical symmetry of identical polymeric subunits in Schönflies notation. Contains point group symbol (e.g., C2, C5, D2, T, O, I) or H for helical symmetry. |
| Type | string |
| Examples | C1 D3 H |
Annotation Id (Assembly Annotation)
| Attribute | rcsb_assembly_annotation.annotation_id |
| Description | An identifier for the annotation. |
| Type | string |
Name (Assembly Annotation) - Mechanism and Catalytic Site Atlas
| Attribute | rcsb_assembly_annotation.name |
| Description | A name for the annotation. |
| Type | string |
| Nested Attribute | rcsb_assembly_annotation.type |
| Nested Attribute Examples | Glutamate racemase Leucyl aminopeptidase |
Oligomeric State
| Attribute | rcsb_struct_symmetry.oligomeric_state |
| Description | Oligomeric state refers to a composition of polymeric subunits in quaternary structure. Quaternary structure may be composed either exclusively of several copies of identical subunits, in which case they are termed homo-oligomers, or alternatively by at least one copy of different subunits (hetero-oligomers). Quaternary structure composed of a single subunit is denoted as 'Monomer'. |
| Type | string |
| Examples | Monomer Homo 2-mer Hetero 3-mer |
Symmetry Type
| Attribute | rcsb_struct_symmetry.type |
| Description | Symmetry type refers to point group or helical symmetry of identical polymeric subunits. Contains point group types (e.g. Cyclic, Dihedral) or Helical for helical symmetry. |
| Type | string |
| Enumeration | Asymmetric Cyclic Dihedral Helical Icosahedral Octahedral Tetrahedral |
Symmetry Class
| Attribute | rcsb_struct_symmetry.kind |
| Description | The granularity at which the symmetry calculation is performed. In 'Global Symmetry' all polymeric subunits in assembly are used. In 'Local Symmetry' only a subset of polymeric subunits is considered. In 'Pseudo Symmetry' the threshold for subunits similarity is relaxed. |
| Type | string |
| Enumeration | Global Symmetry Local Symmetry Pseudo Symmetry |
Protein Symmetry (Browser ID)
| Attribute | rcsb_struct_symmetry_lineage.id |
| Description | Automatically assigned ID to uniquely identify the symmetry term in the Protein Symmetry Browser. |
| Type | string |
| Examples | Global Symmetry.Cyclic.C2.Homo 2-mer |
Methods
Experimental Method
| Attribute | exptl.method |
| Description | The method used in the experiment. |
| Type | string |
| Enumeration | X-RAY DIFFRACTION ELECTRON MICROSCOPY SOLID-STATE NMR SOLUTION NMR NEUTRON DIFFRACTION ELECTRON CRYSTALLOGRAPHY POWDER DIFFRACTION FIBER DIFFRACTION SOLUTION SCATTERING EPR FLUORESCENCE TRANSFER INFRARED SPECTROSCOPY THEORETICAL MODEL |
| Examples | X-RAY DIFFRACTION NEUTRON DIFFRACTION FIBER DIFFRACTION ELECTRON CRYSTALLOGRAPHY ELECTRON MICROSCOPY SOLUTION NMR SOLID-STATE NMR SOLUTION SCATTERING POWDER DIFFRACTION |
Experimental Method (Broader Categories)
| Attribute | rcsb_entry_info.experimental_method |
| Description | The category of experimental method(s) used to determine the structure entry. |
| Type | string |
| Enumeration | EM Multiple methods NMR Neutron Other X-ray |
| Examples | X-ray |
Number of Experimental Methods
| Attribute | rcsb_entry_info.experimental_method_count |
| Description | The number of experimental methods contributing data to the structure determination. |
| Type | integer |
| Minimum Value | 1 |
| Maximum Value | 3 |
Refinement Resolution
| Attribute | rcsb_entry_info.resolution_combined |
| Description | Combined estimates of experimental resolution contributing to the refined structural model. Resolution reported in "refine.ls_d_res_high" is used for X-RAY DIFFRACTION, FIBER DIFFRACTION, POWDER DIFFRACTION, ELECTRON CRYSTALLOGRAPHY, and NEUTRON DIFFRACTION as identified in "refine.pdbx_refine_id". Resolution reported in "em_3d_reconstruction.resolution" is used for ELECTRON MICROSCOPY. The best value corresponding to "em_3d_reconstruction.resolution_method" == "FSC 0.143 CUT-OFF" is used, if available. If not, the best "em_3d_reconstruction.resolution" value is used. For structures that are not obtained from diffraction-based methods, the resolution values in "refine.ls_d_res_high" are ignored. Multiple values are reported only if multiple methods are used in the structure determination. |
| Type | number |
| Minimum Value | 0.48 |
| Maximum Value | 70 |
| Examples | 1.11 2.05 |
Software
| Attribute | rcsb_entry_info.software_programs_combined |
| Description | Combined list of software programs names reported in connection with the production of this entry. |
| Type | string |
| Examples | PHASER PHENIX REFMAC |
Starting Model Type
| Attribute | pdbx_initial_refinement_model.type |
| Description | This item describes the type of the initial model was generated |
| Type | string |
| Enumeration | experimental model in silico model integrative model other |
Starting Model Source
| Attribute | pdbx_initial_refinement_model.source_name |
| Description | This item identifies the resource of initial model used for refinement |
| Type | string |
| Enumeration | AlphaFold ITasser InsightII ModelArchive Modeller Other PDB PDB-Dev PHYRE Robetta RoseTTAFold SwissModel |
Starting Model Accession
| Attribute | pdbx_initial_refinement_model.accession_code |
| Description | This item identifies an accession code of the resource where the initial model is used |
| Type | string |
X-ray Method Details
Structure Determination Method
| Attribute | refine.pdbx_method_to_determine_struct |
| Description | Method(s) used to determine the structure. |
| Type | string |
| Examples | AB INITIO PHASING DM ISAS ISIR ISIRAS MAD MIR MIRAS MR SIR SIRAS |
Average B Factor
| Attribute | refine.B_iso_mean |
| Description | The mean isotropic displacement parameter (B value) for the coordinate set. |
| Type | number |
| Minimum Value | -13.76 |
| Maximum Value | 1274.1 |
Refinement R Factors (Observed)
| Attribute | refine.ls_R_factor_obs |
| Description | Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion. _refine.ls_R_factor_obs should not be confused with _refine.ls_R_factor_R_work; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a 'free' R factor. However, it would be meaningful to quote both values if a 'free' R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in _refine.details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections |
| Type | number |
| Minimum Value | 0.04 |
| Maximum Value | 0.98 |
Refinement R Factors (All)
| Attribute | refine.ls_R_factor_all |
| Description | Residual factor R for all reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections |
| Type | number |
| Minimum Value | 0 |
| Maximum Value | 1 |
Refinement R Factors (R Work)
| Attribute | refine.ls_R_factor_R_work |
| Description | Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. _refine.ls_R_factor_obs should not be confused with _refine.ls_R_factor_R_work; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a 'free' R factor. However, it would be meaningful to quote both values if a 'free' R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in _refine.details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections |
| Type | number |
| Minimum Value | 0.04 |
| Maximum Value | 0.61 |
Refinement R Factors (R Free)
| Attribute | refine.ls_R_factor_R_free |
| Description | Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections |
| Type | number |
| Minimum Value | 0.05 |
| Maximum Value | 0.56 |
Structure Refinement Details
| Attribute | refine.details |
| Description | Description of special aspects of the refinement process. |
| Type | string |
| Examples | HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS |
X-ray Data Collection Details
Data Collection Resolution
| Attribute | rcsb_entry_info.diffrn_resolution_high.value |
| Description | The high resolution limit of data collection. |
| Type | number |
| Minimum Value | 0.48 |
| Maximum Value | 15 |
B Wilson Estimate
| Attribute | reflns.B_iso_Wilson_estimate |
| Description | The value of the overall isotropic displacement parameter estimated from the slope of the Wilson plot. |
| Type | number |
| Minimum Value | -242.62 |
| Maximum Value | 1119.43 |
Overall Redundancy
| Attribute | reflns.pdbx_redundancy |
| Description | Overall redundancy for this data set. |
| Type | number |
| Minimum Value | 0.04 |
| Maximum Value | 26558 |
Percentage of Possible Reflections
| Attribute | reflns.percent_possible_obs |
| Description | The percentage of geometrically possible reflections represented by reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low and the observation limit established by _reflns.observed_criterion. |
| Type | number |
| Minimum Value | 0.04 |
| Maximum Value | 100 |
R Value for Merging Intensities (Observed)
| Attribute | reflns.pdbx_Rmerge_I_obs |
| Description | The R value for merging intensities satisfying the observed criteria in this data set. |
| Type | number |
| Minimum Value | 0 |
| Maximum Value | 9.9 |
Diffraction Detector
| Attribute | diffrn_detector.type |
| Description | The make, model or name of the detector device used. |
| Type | string |
| Examples | DECTRIS PILATUS 12M RAYONIX MX-325 |
Diffraction Source Synchrotron Site
| Attribute | diffrn_source.pdbx_synchrotron_site |
| Description | Synchrotron site. |
| Type | string |
| Examples | APS NSLS-II |
Diffraction Source Synchrotron Beamline
| Attribute | diffrn_source.pdbx_synchrotron_beamline |
| Description | Synchrotron beamline. |
| Type | string |
| Examples | 17-ID-1 19-ID |
Diffraction Source General Class
| Attribute | diffrn_source.source |
| Description | The general class of the radiation source. |
| Type | string |
| Examples | sealed X-ray tube nuclear reactor spallation source electron microscope rotating-anode X-ray tube synchrotron |
Diffraction Source Temperature
| Attribute | diffrn.ambient_temp |
| Description | The mean temperature in kelvins at which the intensities were measured. |
| Type | number |
| Minimum Value | 0 |
| Maximum Value | 446.15 |
Diffraction Serial Crystal Experiment
| Attribute | diffrn.pdbx_serial_crystal_experiment |
| Description | Y/N if using serial crystallography experiment in which multiple crystals contribute to each diffraction frame in the experiment. |
| Type | string |
| Examples | Y N |
Minimum Diffraction Wavelength
| Attribute | rcsb_entry_info.diffrn_radiation_wavelength_minimum |
| Description | The minimum radiation wavelength in angstroms. |
| Type | number |
| Minimum Value | 0 |
| Maximum Value | 81798 |
Maximum Diffraction Wavelength
| Attribute | rcsb_entry_info.diffrn_radiation_wavelength_maximum |
| Description | The maximum radiation wavelength in angstroms. |
| Type | number |
| Minimum Value | 0 |
| Maximum Value | 979257 |
Cell Dimensions and Space Group
Length a
| Attribute | cell.length_a |
| Description | Unit-cell length a corresponding to the structure reported in angstroms. |
| Type | number |
| Minimum Value | 1 |
| Maximum Value | 1255 |
Length b
| Attribute | cell.length_b |
| Description | Unit-cell length b corresponding to the structure reported in angstroms. |
| Type | number |
| Minimum Value | 1 |
| Maximum Value | 1255 |
Length c
| Attribute | cell.length_c |
| Description | Unit-cell length c corresponding to the structure reported in angstroms. |
| Type | number |
| Minimum Value | 1 |
| Maximum Value | 1933.3 |
Angle alpha
| Attribute | cell.angle_alpha |
| Description | Unit-cell angle alpha of the reported structure in degrees. |
| Type | number |
| Minimum Value | 58.8 |
| Maximum Value | 124.81 |
Angle beta
| Attribute | cell.angle_beta |
| Description | Unit-cell angle beta of the reported structure in degrees. |
| Type | number |
| Minimum Value | 45.4 |
| Maximum Value | 164.34 |
Angle gamma
| Attribute | cell.angle_gamma |
| Description | Unit-cell angle gamma of the reported structure in degrees. |
| Type | number |
| Minimum Value | 57.76 |
| Maximum Value | 125 |
Space Group
| Attribute | symmetry.space_group_name_H_M |
| Description | Hermann-Mauguin space-group symbol. Note that the Hermann-Mauguin symbol does not necessarily contain complete information about the symmetry and the space-group origin. If used, always supply the FULL symbol from International Tables for Crystallography Vol. A (2002) and indicate the origin and the setting if it is not implicit. If there is any doubt that the equivalent positions can be uniquely deduced from this symbol, specify the _symmetry_equiv.pos_as_xyz or _symmetry.space_group_name_Hall data items as well. Leave spaces between symbols referring to different axes. |
| Type | string |
| Examples | A 1 A 1 2 1 A 2 B 1 1 2 B 2 B 2 21 2 C 2 C 1 2 1 C 21 C 1 21 1 C 2(A 112) C 2 2 2 C 2 2 21 C 4 21 2 F 2 2 2 F 2 3 F 4 2 2 F 4 3 2 F 41 3 2 I 1 2 1 I 1 21 1 I 2 I 2 2 2 I 2 3 I 21 I 21 3 I 21 21 21 I 4 I 4 2 2 I 4 3 2 I 41 I 41/a I 41 2 2 I 41 3 2 P 1 P 1- P 2 P 1 2 1 P 1 1 2 P 2 2 2 P 2 3 P 2 2 21 P 2 21 21 P 21 P 1 21 1 P 1 21/c 1 P 1 1 21 P 21(C) P 21 2 21 P 21 3 P 21 21 2 P 21 21 2 A P 21 21 21 P 3 P 3 1 2 P 3 2 1 P 31 P 31 1 2 P 31 2 1 P 32 P 32 1 2 P 32 2 1 P 4 P 4 2 2 P 4 3 2 P 4 21 2 P 41 P 41 2 2 P 41 3 2 P 41 21 2 P 42 P 42 2 2 P 42 3 2 P 42 21 2 P 43 P 43 2 2 P 43 3 2 P 43 21 2 P 6 P 6 2 2 P 61 P 61 2 2 P 62 P 62 2 2 P 63 P 63 2 2 P 64 P 64 2 2 P 65 P 65 2 2 H 3 R 3 H 3 2 R 3 2 |
Crystal Properties
Density (Matthews)
| Attribute | exptl_crystal.density_Matthews |
| Description | The density of the crystal, expressed as the ratio of the volume of the asymmetric unit to the molecular mass of a monomer of the structure, in units of angstroms^3^ per dalton. Ref: Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497. |
| Type | number |
| Minimum Value | 0 |
| Maximum Value | 45.14 |
| Examples | 3.1 |
Density (% solvent)
| Attribute | exptl_crystal.density_percent_sol |
| Description | Density value P calculated from the crystal cell and contents, expressed as per cent solvent. P = 1 - (1.23 N MMass) / V N = the number of molecules in the unit cell MMass = the molecular mass of each molecule (gm/mole) V = the volume of the unit cell (A^3^) 1.23 = a conversion factor evaluated as: (0.74 cm^3^/g) (10^24^ A^3^/cm^3^) -------------------------------------- (6.02*10^23^) molecules/mole where 0.74 is an assumed value for the partial specific volume of the molecule |
| Type | number |
| Minimum Value | 0 |
| Maximum Value | 96.06 |
Temperature
| Attribute | exptl_crystal_grow.temp |
| Description | The temperature in kelvins at which the crystal was grown. If more than one temperature was employed during the crystallization process, the final temperature should be noted here and the protocol involving multiple temperatures should be described in _exptl_crystal_grow.details. |
| Type | number |
| Minimum Value | 100 |
| Maximum Value | 328 |
pH
| Attribute | exptl_crystal_grow.pH |
| Description | The pH at which the crystal was grown. If more than one pH was employed during the crystallization process, the final pH should be noted here and the protocol involving multiple pH values should be described in _exptl_crystal_grow.details. |
| Type | number |
| Minimum Value | 0 |
| Maximum Value | 12 |
| Examples | 7.4 7.6 4.3 |
Crystallization Method
| Attribute | exptl_crystal_grow.method |
| Description | The method used to grow the crystals. |
| Type | string |
| Examples | MICROBATCH VAPOR DIFFUSION, HANGING DROP |
Crystallization Details
| Attribute | exptl_crystal_grow.pdbx_details |
| Description | Text description of crystal growth procedure. |
| Type | string |
| Examples | PEG 4000, potassium phosphate, magnesium chloride, cacodylate |
Type of Twinning
| Attribute | pdbx_reflns_twin.type |
| Description | There are two types of twinning: merohedral or hemihedral non-merohedral or epitaxial For merohedral twinning the diffraction patterns from the different domains are completely superimposable. Hemihedral twinning is a special case of merohedral twinning. It only involves two distinct domains. Pseudo-merohedral twinning is a subclass merohedral twinning in which lattice is coincidentally superimposable. In the case of non-merohedral or epitaxial twinning the reciprocal lattices do not superimpose exactly. In this case the diffraction pattern consists of two (or more) interpenetrating lattices, which can in principle be separated. |
| Type | string |
| Enumeration | epitaxial hemihedral merohedral non-merohedral pseudo-merohedral tetartohedral |
EM Method Details
Reconstruction Resolution
| Attribute | em_3d_reconstruction.resolution |
| Description | The final resolution (in angstroms) of the 3D reconstruction. |
| Type | number |
| Minimum Value | 0.6 |
| Maximum Value | 70 |
| Examples | 8.9 10 |
EM Specimen Aggregation State
| Attribute | em_experiment.aggregation_state |
| Description | The aggregation/assembly state of the imaged specimen. |
| Type | string |
| Enumeration | PARTICLE CELL FILAMENT HELICAL ARRAY 2D ARRAY 3D ARRAY TISSUE |
EM Reconstruction Method
| Attribute | em_experiment.reconstruction_method |
| Description | The reconstruction method used in the EM experiment. |
| Type | string |
| Enumeration | CRYSTALLOGRAPHY HELICAL SINGLE PARTICLE SUBTOMOGRAM AVERAGING TOMOGRAPHY |
EM Software
| Attribute | em_software.name |
| Description | The name of the software package used, e.g., RELION. Depositors are strongly encouraged to provide a value in this field. |
| Type | string |
| Examples | EMAN Imagic Spider Bsoft UCSF-Chimera |
EM Vitrification Instrument
| Attribute | em_vitrification.instrument |
| Description | The type of instrument used in the vitrification process. |
| Type | string |
| Enumeration | CRYOSOL VITROJET EMS-002 RAPID IMMERSION FREEZER FEI VITROBOT MARK I FEI VITROBOT MARK II FEI VITROBOT MARK III FEI VITROBOT MARK IV GATAN CRYOPLUNGE 3 HOMEMADE PLUNGER LEICA EM CPC LEICA EM GP LEICA KF80 LEICA PLUNGER REICHERT-JUNG PLUNGER SPOTITON SPT LABTECH CHAMELEON ZEISS PLUNGE FREEZER CRYOBOX |
EM Microscope Model
| Attribute | em_imaging.microscope_model |
| Description | The name of the model of microscope. |
| Type | string |
| Enumeration | FEI MORGAGNI FEI POLARA 300 FEI TALOS ARCTICA FEI TECNAI 10 FEI TECNAI 12 FEI TECNAI 20 FEI TECNAI ARCTICA FEI TECNAI F20 FEI TECNAI F30 FEI TECNAI SPHERA FEI TECNAI SPIRIT FEI TITAN FEI TITAN KRIOS FEI/PHILIPS CM10 FEI/PHILIPS CM12 FEI/PHILIPS CM120T FEI/PHILIPS CM200FEG FEI/PHILIPS CM200FEG/SOPHIE FEI/PHILIPS CM200FEG/ST FEI/PHILIPS CM200FEG/UT FEI/PHILIPS CM200T FEI/PHILIPS CM300FEG/HE FEI/PHILIPS CM300FEG/ST FEI/PHILIPS CM300FEG/T FEI/PHILIPS EM400 FEI/PHILIPS EM420 HITACHI EF2000 HITACHI EF3000 HITACHI H-9500SD HITACHI H3000 UHVEM HITACHI H7600 HITACHI HF2000 HITACHI HF3000 JEOL 1000EES JEOL 100B JEOL 100CX JEOL 1010 JEOL 1200 JEOL 1200EX JEOL 1200EXII JEOL 1230 JEOL 1400 JEOL 1400/HR + YPS FEG JEOL 2000EX JEOL 2000EXII JEOL 2010 JEOL 2010F JEOL 2010HC JEOL 2010HT JEOL 2010UHR JEOL 2011 JEOL 2100 JEOL 2100F JEOL 2200FS JEOL 2200FSC JEOL 3000SFF JEOL 3100FEF JEOL 3100FFC JEOL 3200FS JEOL 3200FSC JEOL 4000 JEOL 4000EX JEOL CRYO ARM 200 JEOL CRYO ARM 300 JEOL KYOTO-3000SFF SIEMENS SULEIKA TFS GLACIOS TFS KRIOS TFS TALOS TFS TALOS F200C TFS TALOS L120C TFS TUNDRA ZEISS LEO912 ZEISS LIBRA120PLUS |
EM Accelerating Voltage
| Attribute | em_imaging.accelerating_voltage |
| Description | A value of accelerating voltage (in kV) used for imaging. |
| Type | integer |
| Minimum Value | 30 |
| Maximum Value | 300300 |
EM Imaging Detector
| Attribute | em_image_recording.film_or_detector_model |
| Description | The detector type used for recording images. Usually film , CCD camera or direct electron detector. |
| Type | string |
EM Point Symmetry Imposed
| Attribute | em_single_particle_entity.point_symmetry |
| Description | Point symmetry symbol, either Cn, Dn, T, O, or I |
| Type | string |
| Examples | C1 C5 C4 |
EM Staining Material
| Attribute | em_staining.material |
| Description | The staining material. |
| Type | string |
| Examples | Uranyl Acetate |
NMR Method Details
NMR Spectrometer Manufacturer
| Attribute | pdbx_nmr_spectrometer.manufacturer |
| Description | The name of the manufacturer of the spectrometer. |
| Type | string |
| Examples | Varian Bruker JEOL GE |
NMR Spectrometer Model
| Attribute | pdbx_nmr_spectrometer.model |
| Description | The model of the NMR spectrometer. |
| Type | string |
| Examples | AVANCE AVANCE II AVANCE III AVANCE III HD WH WM AC+ Alpha AM AMX AMX II DMX DRX DSX MSL OMEGA OMEGA PSG GX GSX A AL EC EX LA ECP Infinityplus Mercury VNMRS VXR UNITY UNITY INOVA UNITYPLUS INOVA home-built |
NMR Spectrometer Field Strength
| Attribute | pdbx_nmr_spectrometer.field_strength |
| Description | The field strength in MHz of the spectrometer |
| Type | number |
| Minimum Value | 0 |
| Maximum Value | 3400 |
NMR Method to Determination Structure
| Attribute | pdbx_nmr_refine.method |
| Description | The method used to determine the structure. |
| Type | string |
| Examples | simulated annealing distance geometry
simulated annealing
molecular dynamics
matrix relaxation
torsion angle dynamics |
Linked External Resources
Experimental Data Resource
| Attribute | rcsb_external_references.type |
| Description | Internal identifier for external resource. |
| Type | string |
| Enumeration | BMRB EM DATA RESOURCE NAKB NDB OLDERADO PROTEIN DIFFRACTION SB GRID |
UniProt-mapped Resource
| Attribute | rcsb_uniprot_external_reference.reference_name |
| Description | |
| Type | string |
| Enumeration | GTEX IMPC PHAROS |
Publications Primary
Primary Citation Author
| Attribute | rcsb_primary_citation.rcsb_authors |
| Description | Names of the authors of the citation; relevant for journal articles, books and book chapters. Names are separated by vertical bars. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). |
| Type | string |
| Examples | Bleary, Percival R. |
Primary Citation Title
| Attribute | rcsb_primary_citation.title |
| Description | The title of the citation; relevant for journal articles, books and book chapters. |
| Type | string |
| Examples | Structure of diferric duck ovotransferrin
at 2.35 Angstroms resolution. |
Primary Citation Journal Name (Abbreviated)
| Attribute | rcsb_primary_citation.rcsb_journal_abbrev |
| Description | Normalized journal abbreviation. |
| Type | string |
| Examples | Nat Struct Mol Biol |
Primary Citation Publication Year
| Attribute | rcsb_primary_citation.year |
| Description | The year of the citation; relevant for journal articles, books and book chapters. |
| Type | integer |
| Minimum Value | 1969 |
| Maximum Value | 2025 |
Primary Citation DOI
| Attribute | rcsb_primary_citation.pdbx_database_id_DOI |
| Description | Document Object Identifier used by doi.org to uniquely specify bibliographic entry. |
| Type | string |
| Examples | 10.2345/S1384107697000225 |
Primary Citation Author ORCID
| Attribute | rcsb_primary_citation.rcsb_ORCID_identifiers |
| Description | The Open Researcher and Contributor ID (ORCID) identifiers for the citation authors. |
| Type | string |
| Examples | 0000-0002-6681-547X |
PubMed Abstract
| Attribute | rcsb_pubmed_abstract_text |
| Description | A concise, accurate and factual mini-version of the paper contents. |
| Type | string |
MeSH Identifier
| Attribute | rcsb_pubmed_mesh_descriptors_lineage.id |
| Description | Identifier for MeSH classification term. |
| Type | string |
| Examples | E01.370.225.500.388 H01.181 |
MeSH Descriptor
| Attribute | rcsb_pubmed_mesh_descriptors_lineage.name |
| Description | MeSH classification term. |
| Type | string |
| Examples | Chemistry Mammals Therapeutic Uses |
Publications All
Citation Author
| Attribute | citation.rcsb_authors |
| Description | Names of the authors of the citation; relevant for journal articles, books and book chapters. Names are separated by vertical bars. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). |
| Type | string |
| Examples | Bleary, Percival R. |
Citation Title
| Attribute | citation.title |
| Description | The title of the citation; relevant for journal articles, books and book chapters. |
| Type | string |
| Examples | Structure of diferric duck ovotransferrin
at 2.35 Angstroms resolution. |
Citation Journal Name (Abbreviated)
| Attribute | citation.rcsb_journal_abbrev |
| Description | Normalized journal abbreviation. |
| Type | string |
| Examples | Nat Struct Mol Biol |
Citation Publication Year
| Attribute | citation.year |
| Description | The year of the citation; relevant for journal articles, books and book chapters. |
| Type | integer |
| Minimum Value | 1947 |
| Maximum Value | 2025 |
Citation DOI
| Attribute | citation.pdbx_database_id_DOI |
| Description | Document Object Identifier used by doi.org to uniquely specify bibliographic entry. |
| Type | string |
| Examples | 10.2345/S1384107697000225 |
Chemical Attributes
Chemical Components
Chemical ID(s)
| Attribute | rcsb_chem_comp_container_identifiers.comp_id |
| Description | The chemical component identifier. |
| Type | string |
| Examples | ATP STI |
| Iterable | true |
Chemical Name
| Attribute | chem_comp.name |
| Description | The full name of the component. |
| Type | string |
| Examples | alanine valine adenine cytosine |
Chemical Synonyms
| Attribute | rcsb_chem_comp_synonyms.name |
| Description | The synonym of this particular chemical component. |
| Type | string |
| Examples | Ursonic acid Talotrexin 4-oxodecanedioic acid |
Chemical Component Release Date
| Attribute | rcsb_chem_comp_info.initial_release_date |
| Description | The initial date the chemical definition was released in the PDB repository. |
| Type | string |
| Minimum Value | 1973-05-03 |
| Maximum Value | 2024-12-18 |
| Examples | 2016-09-11 |
Chemical Component Type
| Attribute | chem_comp.type |
| Description | For standard polymer components, the type of the monomer. Note that monomers that will form polymers are of three types: linking monomers, monomers with some type of N-terminal (or 5') cap and monomers with some type of C-terminal (or 3') cap. |
| Type | string |
| Enumeration | D-beta-peptide, C-gamma linking D-gamma-peptide, C-delta linking D-peptide COOH carboxy terminus D-peptide NH3 amino terminus D-peptide linking D-saccharide D-saccharide, alpha linking D-saccharide, beta linking DNA OH 3 prime terminus DNA OH 5 prime terminus DNA linking L-DNA linking L-RNA linking L-beta-peptide, C-gamma linking L-gamma-peptide, C-delta linking L-peptide COOH carboxy terminus L-peptide NH3 amino terminus L-peptide linking L-saccharide L-saccharide, alpha linking L-saccharide, beta linking RNA OH 3 prime terminus RNA OH 5 prime terminus RNA linking non-polymer other peptide linking peptide-like saccharide |
Drug Target Name
| Attribute | rcsb_chem_comp_target.name |
| Description | The chemical component target name. |
| Type | string |
Drug Brand Name
| Attribute | drugbank_info.brand_names |
| Description | DrugBank drug brand names. |
| Type | string |
| Examples | Atriphos; Striadyne |
Drug Groups
| Attribute | drugbank_info.drug_groups |
| Description | The DrugBank drug groups determine their drug development status. |
| Type | string |
| Enumeration | approved experimental illicit investigational nutraceutical vet_approved withdrawn |
| Examples | approved nutraceutical |
Drug Is Approved
| Attribute | drugbank_info.drug_products.approved |
| Description | Indicates whether this drug has been approved by the regulating government. |
| Type | string |
| Enumeration | N Y |
Drug Marketing Start
| Attribute | drugbank_info.drug_products.started_marketing_on |
| Description | The starting date for market approval. |
| Type | string |
| Minimum Value | 1880-01-01 |
| Maximum Value | 2077-01-01 |
| Examples | 1992-12-31 |
Drug Marketing End
| Attribute | drugbank_info.drug_products.ended_marketing_on |
| Description | The ending date for market approval. |
| Type | string |
| Minimum Value | 1936-01-02 |
| Maximum Value | 2050-08-02 |
| Examples | 2003-07-30 |
Drug Market Availability
| Attribute | drugbank_info.drug_products.country |
| Description | The country where this commercially available drug has been approved. |
| Type | string |
| Enumeration | Canada EU US |
| Examples | Canada |
InChiKey
| Attribute | rcsb_chem_comp_descriptor.InChIKey |
| Description | Standard IUPAC International Chemical Identifier (InChI) descriptor key for the chemical component InChI, the IUPAC International Chemical Identifier, by Stephen R Heller, Alan McNaught, Igor Pletnev, Stephen Stein and Dmitrii Tchekhovskoi, Journal of Cheminformatics, 2015, 7:23 |
| Type | string |
| Examples | BNOCDEBUFVJMQI-REOHCLBHSA-N |
Chemical Component Molecular Weight
| Attribute | chem_comp.formula_weight |
| Description | Formula mass of the chemical component. |
| Type | number |
| Minimum Value | 2.01 |
| Maximum Value | 12016 |
| Examples | 120.12 450.1 |
Chemical Component Nonhydrogen Atom Count
| Attribute | rcsb_chem_comp_info.atom_count_heavy |
| Description | Chemical component heavy atom count |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 352 |
Chemical Component Chiral Atom Count
| Attribute | rcsb_chem_comp_info.atom_count_chiral |
| Description | Chemical component chiral atom count |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 52 |
Chemical Component Bond Count
| Attribute | rcsb_chem_comp_info.bond_count |
| Description | Chemical component total bond count |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 727 |
Chemical Component Aromatic Bond Count
| Attribute | rcsb_chem_comp_info.bond_count_aromatic |
| Description | Chemical component aromatic bond count |
| Type | integer |
| Minimum Value | 0 |
| Maximum Value | 116 |
Identifier Codes - DrugBank
| Attribute | rcsb_chem_comp_related.resource_accession_code |
| Description | The resource identifier code for the related chemical reference. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_related.resource_name |
| Nested Attribute Examples | DB06830 DB07255 |
Identifier Codes - CCDC/CSD
| Attribute | rcsb_chem_comp_related.resource_accession_code |
| Description | The resource identifier code for the related chemical reference. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_related.resource_name |
| Nested Attribute Examples | QAXDEZ XEGJEA |
Identifier Codes - COD
| Attribute | rcsb_chem_comp_related.resource_accession_code |
| Description | The resource identifier code for the related chemical reference. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_related.resource_name |
| Nested Attribute Examples | 2236573 7229993 |
Identifier Codes - RESID
| Attribute | rcsb_chem_comp_related.resource_accession_code |
| Description | The resource identifier code for the related chemical reference. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_related.resource_name |
| Nested Attribute Examples | AA0078 AA0034 |
Identifier Codes - PubChem
| Attribute | rcsb_chem_comp_related.resource_accession_code |
| Description | The resource identifier code for the related chemical reference. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_related.resource_name |
| Nested Attribute Examples | 3082729 5289380 |
Identifier Codes - ChEBI
| Attribute | rcsb_chem_comp_related.resource_accession_code |
| Description | The resource identifier code for the related chemical reference. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_related.resource_name |
| Nested Attribute Examples | CHEBI:151557 CHEBI:6198 |
Identifier Codes - ChEMBL
| Attribute | rcsb_chem_comp_related.resource_accession_code |
| Description | The resource identifier code for the related chemical reference. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_related.resource_name |
| Nested Attribute Examples | CHEMBL1165239 CHEMBL3330255 |
Identifier Codes - CAS Registry Number
| Attribute | rcsb_chem_comp_related.resource_accession_code |
| Description | The resource identifier code for the related chemical reference. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_related.resource_name |
| Nested Attribute Examples | 2133-34-8 30565-25-4 |
Identifier Codes - Pharos
| Attribute | rcsb_chem_comp_related.resource_accession_code |
| Description | The resource identifier code for the related chemical reference. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_related.resource_name |
| Nested Attribute Examples | CHEMBL1165239 CHEMBL3330255 |
Name - RESID Generating Enzyme
| Attribute | rcsb_chem_comp_annotation.name |
| Description | A name for the annotation. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_annotation.type |
| Nested Attribute Examples | protein N-terminal methyltransferase (EC 2.1.1.-) autocatalytic |
Name - RESID Modification
| Attribute | rcsb_chem_comp_annotation.name |
| Description | A name for the annotation. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_annotation.type |
| Nested Attribute Examples | Thyroxine N4-methylasparagine |
Name - Carbohydrate Anomer
| Attribute | rcsb_chem_comp_annotation.name |
| Description | A name for the annotation. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_annotation.type |
| Nested Attribute Examples | alpha beta |
Name - Carbohydrate Isomer
| Attribute | rcsb_chem_comp_annotation.name |
| Description | A name for the annotation. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_annotation.type |
| Nested Attribute Examples | D L |
Name - Carbohydrate Ring
| Attribute | rcsb_chem_comp_annotation.name |
| Description | A name for the annotation. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_annotation.type |
| Nested Attribute Examples | pyranose furanose |
Name - Carbohydrate Primary Carbonyl Group
| Attribute | rcsb_chem_comp_annotation.name |
| Description | A name for the annotation. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_annotation.type |
| Nested Attribute Examples | aldose ketose |
Lineage Name - ATC (WHO)
| Attribute | rcsb_chem_comp_annotation.annotation_lineage.name |
| Description | Members of the annotation lineage as parent class names. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_annotation.type |
| Nested Attribute Examples | lisuride etacrynic acid |
Lineage Name - PSI-MOD
| Attribute | rcsb_chem_comp_annotation.annotation_lineage.name |
| Description | Members of the annotation lineage as parent class names. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_annotation.type |
| Nested Attribute Examples | monomethylated residue alpha-amino monomethylated residue |
Lineage Identifier - ATC (WHO)
| Attribute | rcsb_chem_comp_annotation.annotation_lineage.id |
| Description | Members of the annotation lineage as parent class identifiers. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_annotation.type |
| Nested Attribute Examples | G02CB02 C03CC01 |
Lineage Identifier - PSI-MOD
| Attribute | rcsb_chem_comp_annotation.annotation_lineage.id |
| Description | Members of the annotation lineage as parent class identifiers. |
| Type | string |
| Nested Attribute | rcsb_chem_comp_annotation.type |
| Nested Attribute Examples | MOD:00599 MOD:01680 |
Biologically Interesting Molecules (BIRD)
BIRD ID(s)
| Attribute | pdbx_reference_molecule.prd_id |
| Description | The value of _pdbx_reference_molecule.prd_id is the unique identifier for the reference molecule in this family. By convention this ID uniquely identifies the reference molecule in in the PDB reference dictionary. The ID has the template form PRD_dddddd (e.g. PRD_000001) |
| Type | string |
| Examples | PRD_000001 PRD_0000010 |
| Iterable | true |
BIRD Name
| Attribute | pdbx_reference_molecule.name |
| Description | A name of the entity. |
| Type | string |
| Examples | thiostrepton |
BIRD Type
| Attribute | pdbx_reference_molecule.type |
| Description | Defines the structural classification of the entity. |
| Type | string |
| Enumeration | Amino acid Aminoglycoside Ansamycin Anthracycline Anthraquinone Chalkophore Chalkophore, Polypeptide Chromophore Cyclic depsipeptide Cyclic lipopeptide Cyclic peptide Glycopeptide Heterocyclic Imino sugar Keto acid Lipoglycopeptide Lipopeptide Macrolide Non-polymer Nucleoside Oligopeptide Oligosaccharide Peptaibol Peptide-like Polycyclic Polypeptide Polysaccharide Quinolone Siderophore Thiolactone Thiopeptide Unknown |
| Examples | Peptide-like Macrolide |
BIRD Class
| Attribute | pdbx_reference_molecule.class |
| Description | Broadly defines the function of the entity. |
| Type | string |
| Enumeration | Antagonist Anthelmintic Antibiotic Antibiotic, Anthelmintic Antibiotic, Antimicrobial Antibiotic, Antineoplastic Anticancer Anticoagulant Anticoagulant, Antithrombotic Antifungal Antigen Antiinflammatory Antimicrobial Antimicrobial, Antiparasitic, Antibiotic Antimicrobial, Antiretroviral Antimicrobial, Antitumor Antineoplastic Antiparasitic Antiretroviral Antithrombotic Antitumor Antiviral CASPASE inhibitor Chaperone binding Drug delivery Enzyme inhibitor Glycan component Growth factor Immunosuppressant Inducer Inhibitor Lantibiotic Metabolism Metal transport Nutrient Oxidation-reduction Protein binding Receptor Substrate analog Synthetic opioid Thrombin inhibitor Thrombin inhibitor, Trypsin inhibitor Toxin Transition state mimetic Transport activator Trypsin inhibitor Unknown Water retention |
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Last updated: Tue Dec 17 2024
