By Scientific Name of Source Organism
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, and includes natural, engineered, and synthetic source organisms.
Scientific Name of Source Organism | Number of Entries |
---|---|
Homo sapiens | 57185 |
Mus musculus | 7958 |
Escherichia coli | 6676 |
synthetic construct | 6669 |
Escherichia coli K-12 | 3952 |
Rattus norvegicus | 3581 |
Bos taurus | 3399 |
Saccharomyces cerevisiae | 3071 |
Gallus gallus | 2196 |
Saccharomyces cerevisiae S288C | 2185 |
Severe acute respiratory syndrome coronavirus 2 | 2131 |
Human immunodeficiency virus 1 | 1935 |
Arabidopsis thaliana | 1787 |
Mycobacterium tuberculosis H37Rv | 1468 |
Staphylococcus aureus | 1429 |
Mycobacterium tuberculosis | 1354 |
Thermus thermophilus HB8 | 1272 |
Bacillus subtilis | 1213 |
Pseudomonas aeruginosa | 1182 |
Drosophila melanogaster | 1175 |
Sus scrofa | 1161 |
Pseudomonas aeruginosa PAO1 | 1127 |
Oryctolagus cuniculus | 1068 |
Escherichia virus T4 | 1036 |
Cryphonectria parasitica | 754 |
Thermotoga maritima | 713 |
Thermus thermophilus | 665 |
Geobacillus stearothermophilus | 639 |
Bacillus subtilis subsp. subtilis str. 168 | 610 |
Salmonella enterica subsp. enterica serovar Typhimurium | 565 |
Pseudomonas putida | 558 |
Klebsiella pneumoniae | 551 |
Lama glama | 535 |
Danio rerio | 513 |
Aequorea victoria | 495 |
Plasmodium falciparum 3D7 | 469 |
Mycolicibacterium smegmatis MC2 155 | 452 |
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 | 452 |
Pyrococcus horikoshii OT3 | 445 |
Plasmodium falciparum | 438 |
Xenopus laevis | 436 |
Thermotoga maritima MSB8 | 432 |
Caenorhabditis elegans | 426 |
Equus caballus | 406 |
Saccharolobus solfataricus | 335 |
Pyrococcus furiosus | 329 |
Physeter catodon | 324 |
Vibrio cholerae | 317 |
Aquifex aeolicus | 304 |
Hirudo medicinalis | 303 |
Archaeoglobus fulgidus | 302 |
Bacteroides thetaiotaomicron VPI-5482 | 301 |
Escherichia coli O157:H7 | 292 |
Methanocaldococcus jannaschii | 291 |
Streptococcus pneumoniae | 291 |
Saccharolobus solfataricus P2 | 288 |
Acinetobacter baumannii | 285 |
Trypanosoma brucei | 283 |
Influenza A virus | 281 |
Aquifex aeolicus VF5 | 272 |
Trypanosoma cruzi | 272 |
Chaetomium thermophilum var. thermophilum DSM 1495 | 267 |
Haemophilus influenzae | 266 |
unidentified | 262 |
Bacillus anthracis | 261 |
Streptomyces avidinii | 258 |
Chlamydomonas reinhardtii | 256 |
Helicobacter pylori | 256 |
Streptococcus pneumoniae TIGR4 | 255 |
Helicobacter pylori 26695 | 239 |
Thermus thermophilus HB27 | 239 |
Bacillus cereus | 236 |
Schizosaccharomyces pombe 972h- | 235 |
Agrobacterium fabrum str. C58 | 227 |
Hepacivirus C | 227 |
Severe acute respiratory syndrome-related coronavirus | 225 |
Vibrio cholerae O1 biovar El Tor str. N16961 | 224 |
Zea mays | 223 |
Pyrococcus horikoshii | 220 |
Escherichia coli BL21(DE3) | 219 |
Schizosaccharomyces pombe | 216 |
Leishmania major | 215 |
Clostridium botulinum | 212 |
Trypanosoma brucei brucei | 210 |
Enterococcus faecalis | 209 |
Ovis aries | 208 |
Parengyodontium album | 208 |
Schistosoma mansoni | 207 |
Bacillus thermoproteolyticus | 204 |
Legionella pneumophila subsp. pneumophila str. Philadelphia 1 | 203 |
Cereibacter sphaeroides | 201 |
Methanocaldococcus jannaschii DSM 2661 | 199 |
Streptomyces coelicolor A3(2) | 196 |
Priestia megaterium | 195 |
Yersinia pestis | 195 |
Dictyostelium discoideum | 193 |
Pyrococcus furiosus DSM 3638 | 189 |
Staphylococcus aureus subsp. aureus Mu50 | 189 |
Campylobacter jejuni | 187 |
Listeria monocytogenes EGD-e | 186 |
By Taxonomy
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.
Taxonomy | Number of Entries |
---|---|
Eukaryota | 104101 |
Bacteria | 65569 |
Riboviria | 11068 |
other sequences | 6730 |
Archaea | 5637 |
Duplodnaviria | 2728 |
Varidnaviria | 627 |
Monodnaviria | 518 |
unclassified sequences | 382 |
Naldaviricetes | 48 |
unclassified bacterial viruses | 44 |
Adnaviria | 33 |
Bicaudaviridae | 17 |
Fuselloviridae | 11 |
unclassified viruses | 11 |
Ribozyviria | 7 |
environmental samples | 7 |
Globuloviridae | 5 |
Polydnaviridae | 2 |
Clavaviridae | 1 |
Portogloboviridae | 1 |
By Polymer Entity Type
PDB structures may contain multiple entities of different macromolecular types.
By Refinement Resolution (Å)
Distribution by structure resolution (Å). Data shown include structures solved by X-ray crystallography or electron microscopy.
By Release Date
The year a structure entry was released in the PDB archive.
By Enzyme Classification Name
Enzyme Classification is based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB). EC (Enzyme Commission) numbers are assigned to PDB structures using UniProtKB/GenBank/KEGG/author-specified mapping.
By Symmetry Type
Protein symmetry is calculated for all protein complexes in the PDB, and updated weekly.
By SCOP Classification
The SCOP database aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.
- Alpha and beta proteins (a/b) (33557)
- All beta proteins (29551)
- Alpha and beta proteins (a+b) (30493)
- All alpha proteins (19132)
- Artifacts (19314)
- Multi-domain proteins (alpha and beta) (3462)
- Membrane and cell surface proteins and peptides (2051)
- Small proteins (3765)
- Coiled coil proteins (981)
- Others (1124)
SCOP Classification | Number of Entries |
---|---|
Alpha and beta proteins (a/b) | 33557 |
All beta proteins | 29551 |
Alpha and beta proteins (a+b) | 30493 |
All alpha proteins | 19132 |
Artifacts | 19314 |
Multi-domain proteins (alpha and beta) | 3462 |
Membrane and cell surface proteins and peptides | 2051 |
Small proteins | 3765 |
Coiled coil proteins | 981 |
Low resolution protein structures | 202 |
Peptides | 754 |
Designed proteins | 168 |