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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "van den Bedem, H."

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Search Summary

This query matches 215 Structures.

Refinements

Structure Determination Methodology

experimental (215)

Scientific Name of Source Organism

	Homo sapiens (40)
	Thermotoga maritima (30)
	Pseudomonas protegens Pf-5 (28)
	Gallus gallus (14)
	Thaumatococcus daniellii (9)
	Thermotoga maritima MSB8 (9)
	Mus musculus (7)
	Helicobacter pylori (6)
	Bacteroides thetaiotaomicron VPI-5482 (5)
	Escherichia coli K-12 (5)

More...

Taxonomy

	Bacteria (136)
	Eukaryota (74)
	Archaea (4)
	unclassified sequences (1)

Experimental Method

	X-RAY DIFFRACTION (208)
	ELECTRON MICROSCOPY (6)
	ELECTRON CRYSTALLOGRAPHY (1)

Polymer Entity Type

Protein (215)

Refinement Resolution (Å)

	0.5 - 1.0 (2)
	1.0 - 1.5 (69)
	1.5 - 2.0 (87)
	2.0 - 2.5 (35)
	2.5 - 3.0 (14)
	3.0 - 3.5 (4)
	3.5 - 4.0 (4)

Release Date

	2000 - 2004 (37)
	2005 - 2009 (58)
	2010 - 2014 (15)
	2015 - 2019 (82)
	2020 - 2024 (23)

Enzyme Classification Name

	Isomerases (37)
	Hydrolases (29)
	Oxidoreductases (14)
	Transferases (12)
	Lyases (8)
	Ligases (4)

Membrane Protein Annotation

	mpstruc (6)
	OPM (5)

Symmetry Type

	Asymmetric (121)
	Cyclic (90)
	Dihedral (18)

SCOP Classification

	All beta proteins (60)
	Alpha and beta proteins (a/b) (42)
	Artifacts (41)
	Alpha and beta proteins (a+b) (44)
	All alpha proteins (18)
	Multi-domain proteins (alpha and beta) (3)
	Small proteins (2)

AllSelected

1 to 25 of 215 Structures

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1J5S \| pdb_00001j5s	Download File View File

Crystal structure of uronate isomerase (TM0064) from Thermotoga maritima at 2.85 A resolution

Joint Center for Structural Genomics (JCSG)

(2003) Proteins 53: 142-145

Released	2002-07-17
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Thermotoga maritima
Macromolecule	URONATE ISOMERASE (protein)

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1J5Y \| pdb_00001j5y	Download File View File

Crystal structure of transcriptional regulator (TM1602) from Thermotoga maritima at 2.3 A resolution

Joint Center for Structural Genomics (JCSG)

(2007) Proteins 67: 247-252

Released	2002-07-31
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Thermotoga maritima
Macromolecule	TRANSCRIPTIONAL REGULATOR, BIOTIN REPRESSOR FAMILY (protein)
Unique Ligands	K, NI

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1J6U \| pdb_00001j6u	Download File View File

Crystal structure of UDP-N-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 55: 1078-1081

Released	2002-11-06
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Thermotoga maritima
Macromolecule	UDP-N-acetylmuramate-alanine ligase MurC (protein)

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1O0X \| pdb_00001o0x	Download File View File

Crystal structure of Methionine aminopeptidase (TM1478) from Thermotoga maritima at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 56: 396-400

Released	2002-11-06
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermotoga maritima
Macromolecule	Methionine aminopeptidase (protein)

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1O1X \| pdb_00001o1x	Download File View File

Crystal structure of a ribose 5-phosphate isomerase rpib (tm1080) from thermotoga maritima at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 56: 171-175

Released	2003-04-01
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermotoga maritima
Macromolecule	ribose-5-phosphate isomerase RpiB (protein)
Unique Ligands	MPD

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1O1Y \| pdb_00001o1y	Download File View File

Crystal structure of a glutamine amidotransferase (tm1158) from thermotoga maritima at 1.70 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 54: 801-805

Released	2003-03-11
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Thermotoga maritima
Macromolecule	conserved hypothetical protein TM1158 (protein)
Unique Ligands	SO4

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1O1Z \| pdb_00001o1z	Download File View File

Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) (TM1621) from Thermotoga maritima at 1.60 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 56: 167-170

Released	2003-04-01
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Thermotoga maritima
Macromolecule	glycerophosphodiester phosphodiesterase (protein)
Unique Ligands	NA

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1O20 \| pdb_00001o20	Download File View File

Crystal structure of Gamma-glutamyl phosphate reductase (TM0293) from Thermotoga maritima at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 54: 157-161

Released	2003-04-01
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thermotoga maritima
Macromolecule	Gamma-glutamyl phosphate reductase (protein)

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1O22 \| pdb_00001o22	Download File View File

Crystal structure of an orphan protein (TM0875) from Thermotoga maritima at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 56: 607-610

Released	2003-04-01
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thermotoga maritima
Macromolecule	orphan protein TM0875 (protein)

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1O2D \| pdb_00001o2d	Download File View File

Crystal structure of Alcohol dehydrogenase, iron-containing (TM0920) from Thermotoga maritima at 1.30 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 54: 174-177

Released	2003-06-10
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Thermotoga maritima
Macromolecule	Alcohol dehydrogenase, iron-containing (protein)
Unique Ligands	FE, NAP, TRS

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1O3U \| pdb_00001o3u	Download File View File

Crystal structure of an hepn domain protein (tm0613) from thermotoga maritima at 1.75 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 54: 806-809

Released	2003-04-22
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Thermotoga maritima
Macromolecule	conserved hypothetical protein TM0613 (protein)

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1O4S \| pdb_00001o4s	Download File View File

Crystal structure of Aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 55: 759-763

Released	2003-07-08
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermotoga maritima
Macromolecule	Aspartate aminotransferase (protein)
Unique Ligands	PLP, SO4

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1O4T \| pdb_00001o4t	Download File View File

Crystal structure of a predicted oxalate decarboxylase (tm1287) from thermotoga maritima at 1.95 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 56: 392-395

Released	2003-07-15
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Thermotoga maritima
Macromolecule	putative oxalate decarboxylase (protein)
Unique Ligands	MN, OXL

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1O4U \| pdb_00001o4u	Download File View File

Crystal structure of a nicotinate nucleotide pyrophosphorylase (tm1645) from thermotoga maritima at 2.50 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 55: 768-771

Released	2003-07-22
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermotoga maritima
Macromolecule	Type II quinolic acid phosphoribosyltransferase (protein)

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1O4V \| pdb_00001o4v	Download File View File

Crystal structure of the catalytic subunit of a phosphoribosylaminoimidazole mutase (tm0446) from thermotoga maritima at 1.77 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 55: 474-478

Released	2003-07-22
Method	X-RAY DIFFRACTION 1.77 Å
Organisms	Thermotoga maritima
Macromolecule	phosphoribosylaminoimidazole mutase PurE (protein)
Unique Ligands	SO4

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1O4W \| pdb_00001o4w	Download File View File

CRYSTAL STRUCTURE OF a PIN (PILT N-TERMINUS) DOMAIN CONTAINING PROTEIN (AF0591) FROM ARCHAEOGLOBUS FULGIDUS AT 1.90 A RESOLUTION

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 56: 404-408

Released	2003-07-29
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	PIN (PilT N-terminus) domain (protein)

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1O50 \| pdb_00001o50	Download File View File

Crystal structure of a cbs domain-containing protein (tm0935) from thermotoga maritima at 1.87 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 57: 213-217

Released	2003-08-12
Method	X-RAY DIFFRACTION 1.87 Å
Organisms	Thermotoga maritima
Macromolecule	CBS domain-containing predicted protein TM0935 (protein)

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1O51 \| pdb_00001o51	Download File View File

Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.50 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 54: 810-813

Released	2003-08-19
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermotoga maritima
Macromolecule	Hypothetical protein TM0021 (protein)
Unique Ligands	ADP, SO4

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1O58 \| pdb_00001o58	Download File View File

Crystal structure of O-acetylserine sulfhydrylase (TM0665) from Thermotoga maritima at 1.80 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 56: 387-391

Released	2003-09-02
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermotoga maritima
Macromolecule	O-acetylserine sulfhydrylase (protein)
Unique Ligands	PO4

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1O59 \| pdb_00001o59	Download File View File

Crystal structure of Allantoicase (yir029w) from Saccharomyces cerevisiae at 2.40 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 56: 619-624

Released	2003-09-02
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Allantoicase (protein)

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1O5H \| pdb_00001o5h	Download File View File

Crystal structure of formiminotetrahydrofolate cyclodeaminase (TM1560) from Thermotoga maritima at 2.80 A resolution

Joint Center for Structural Genomics (JCSG)

(2005) Proteins 58: 976-981

Released	2003-09-30
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Thermotoga maritima
Macromolecule	Formiminotetrahydrofolate cyclodeaminase (protein)

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1O5U \| pdb_00001o5u	Download File View File

Crystal structure of a duf861 family protein (tm1112) from thermotoga maritima at 1.83 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 56: 615-618

Released	2003-11-11
Method	X-RAY DIFFRACTION 1.83 Å
Organisms	Thermotoga maritima
Macromolecule	novel Thermotoga maritima enzyme TM1112 (protein)
Unique Ligands	UNL

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1VJ1 \| pdb_00001vj1	Download File View File

Crystal structure of putative NADPH-dependent oxidoreductase from Mus musculus at 2.10 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 56: 629-633

Released	2003-12-09
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Mus musculus
Macromolecule	putative NADPH-dependent oxidoreductase (protein)

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1VJ2 \| pdb_00001vj2	Download File View File

Crystal structure of a novel family of manganese-containing cupin (tm1459) from thermotoga maritima at 1.65 A resolution

Joint Center for Structural Genomics (JCSG)

(2004) Proteins 56: 611-614

Released	2003-12-09
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Thermotoga maritima
Macromolecule	novel manganese-containing cupin TM1459 (protein)
Unique Ligands	MN, UNL

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1VJO \| pdb_00001vjo	Download File View File

Crystal structure of Alanine--glyoxylate aminotransferase (ALR1004) from Nostoc sp. at 1.70 A resolution

Joint Center for Structural Genomics (JCSG)

(2005) Proteins 58: 971-975

Released	2004-03-23
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Nostoc sp. PCC 7120 = FACHB-418
Macromolecule	alanine--glyoxylate aminotransferase (protein)
Unique Ligands	PLP

1 to 25 of 215 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1J5S | pdb_00001j5s

1J5Y | pdb_00001j5y

1J6U | pdb_00001j6u

1O0X | pdb_00001o0x

1O1X | pdb_00001o1x

1O1Y | pdb_00001o1y

1O1Z | pdb_00001o1z

1O20 | pdb_00001o20

1O22 | pdb_00001o22

1O2D | pdb_00001o2d

1O3U | pdb_00001o3u

1O4S | pdb_00001o4s

1O4T | pdb_00001o4t

1O4U | pdb_00001o4u

1O4V | pdb_00001o4v

1O4W | pdb_00001o4w

1O50 | pdb_00001o50

1O51 | pdb_00001o51

1O58 | pdb_00001o58

1O59 | pdb_00001o59

1O5H | pdb_00001o5h

1O5U | pdb_00001o5u

1VJ1 | pdb_00001vj1

1VJ2 | pdb_00001vj2

1VJO | pdb_00001vjo