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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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Search Summary

This query matches 421 Structures.

Refinements

Structure Determination Methodology

experimental (421)

Scientific Name of Source Organism

	Homo sapiens (132)
	Thermochaetoides thermophila DSM 1495 (24)
	Mus musculus (16)
	Escherichia coli K-12 (11)
	Escherichia coli (10)
	DNA molecule (6)
	Mycobacterium tuberculosis H37Rv (6)
	Niallia circulans subsp. circulans (6)
	Paradendryphiella salina (5)
	Plasmodium falciparum 3D7 (5)

More...

Taxonomy

	Eukaryota (235)
	Bacteria (171)
	Riboviria (6)
	unclassified sequences (6)
	Archaea (5)
	Duplodnaviria (5)
	other sequences (2)
	Eukaryota (eukaryotes) (1)
	Viruses incertae sedis (1)

Experimental Method

X-RAY DIFFRACTION (421)

Polymer Entity Type

	Protein (421)
	DNA (10)
	NA-hybrid (2)

Refinement Resolution (Å)

	0.5 - 1.0 (4)
	1.0 - 1.5 (68)
	1.5 - 2.0 (198)
	2.0 - 2.5 (126)
	2.5 - 3.0 (22)
	3.0 - 3.5 (3)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (9)
	2005 - 2009 (44)
	2010 - 2014 (69)
	2015 - 2019 (114)
	2020 - 2024 (177)
	2025 - 2029 (7)

Enzyme Classification Name

	Hydrolases (130)
	Oxidoreductases (94)
	Transferases (62)
	Lyases (19)
	Isomerases (16)
	Ligases (3)
	Translocases (1)

Membrane Protein Annotation

OPM (2)

Symmetry Type

	Asymmetric (226)
	Cyclic (175)
	Dihedral (35)
	Octahedral (1)

SCOP Classification

	All beta proteins (45)
	Alpha and beta proteins (a+b) (58)
	Alpha and beta proteins (a/b) (56)
	All alpha proteins (23)
	Artifacts (18)
	Small proteins (7)
	Membrane and cell surface proteins and peptides (1)

AllSelected

1 to 25 of 421 Structures

Page 1 of 17

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1AG9 \| pdb_00001ag9	Download File View File

FLAVODOXINS THAT ARE REQUIRED FOR ENZYME ACTIVATION: THE STRUCTURE OF OXIDIZED FLAVODOXIN FROM ESCHERICHIA COLI AT 1.8 ANGSTROMS RESOLUTION.

Hoover, D.M., Ludwig, M.L.

(1997) Protein Sci 6: 2525-2537

Released	1997-12-24
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli
Macromolecule	FLAVODOXIN (protein)
Unique Ligands	BTB, CA, CL, FMN, NA

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1JZ2 \| pdb_00001jz2	Download File View File

E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-F-GALACTOSYL-ENZYME INTERMEDIATE (ORTHORHOMBIC)

Juers, D.H., McCarter, J.D., Mackenzie, L., Withers, S.G., Matthews, B.W.

(2001) Biochemistry 40: 14781-14794

Released	2001-12-07
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli
Macromolecule	Beta-Galactosidase (protein)
Unique Ligands	2FG, BTB, DMS, MG, NA

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1JZ3 \| pdb_00001jz3	Download File View File

E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-DEOXY-GALACTOSYL ENZYME INTERMEDIATE

Juers, D.H., Matthews, B.W.

(2001) Biochemistry 40: 14781-14794

Released	2001-12-07
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Escherichia coli
Macromolecule	Beta-Galactosidase (protein)
Unique Ligands	2DG, BTB, DMS, MG, NA

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1N1Z \| pdb_00001n1z	Download File View File

(+)-Bornyl Diphosphate Synthase: Complex with Mg and pyrophosphate

Whittington, D.A., Wise, M.L., Urbansky, M., Coates, R.M., Croteau, R.B., Christianson, D.W.

(2002) Proc Natl Acad Sci U S A 99: 15375-15380

Released	2002-11-27
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Salvia officinalis
Macromolecule	(+)-bornyl diphosphate synthase (protein)
Unique Ligands	BTB, MG, POP

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1R64 \| pdb_00001r64	Download File View File

The 2.2 A crystal structure of Kex2 protease in complex with Ac-Arg-Glu-Lys-boroArg peptidyl boronic acid inhibitor

Holyoak, T., Kettner, C.A., Petsko, G.A., Fuller, R.S., Ringe, D.

(2004) Biochemistry 43: 2412-2421

Released	2004-03-09
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Ac-Arg-Glu-Lys-boroArg peptide inhibitor (protein) Kexin (protein)
Unique Ligands	BTB, CA, K, NAG
Unique branched monosaccharides	NAG

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1RJ4 \| pdb_00001rj4	Download File View File

Structure of a Cell Wall Invertase Inhibitor from Tobacco in Complex with Cd2+

Hothorn, M., D'Angelo, I., Marquez, J.A., Greiner, S., Scheffzek, K.

(2004) J Mol Biology 335: 987-995

Released	2004-02-03
Method	X-RAY DIFFRACTION 2 Å
Organisms	Nicotiana tabacum
Macromolecule	invertase inhibitor (protein)
Unique Ligands	BTB, CD

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1TW6 \| pdb_00001tw6	Download File View File

Structure of an ML-IAP/XIAP chimera bound to a 9mer peptide derived from Smac

Franklin, M.C., Vucic, D., Wallweber, H.J.A., Das, K., Shin, H., Elliott, L.O., Kadkhodayan, S., Deshayes, K., Salvesen, G.S., Fairbrother, W.J.

(2005) Biochem J 385: 11-20

Released	2004-11-02
Method	X-RAY DIFFRACTION 1.713 Å
Organisms	Homo sapiens
Macromolecule	Baculoviral IAP repeat-containing protein 7 (protein) Diablo homolog, mitochondrial (protein)
Unique Ligands	BTB, EDO, LI, ZN

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1VCL \| pdb_00001vcl	Download File View File

Crystal Structure of Hemolytic Lectin CEL-III

Uchida, T., Yamasaki, T., Eto, S., Sugawara, H., Kurisu, G., Nakagawa, A., Kusunoki, M., Hatakeyama, T.

(2004) J Biological Chem 279: 37133-37141

Released	2004-09-07
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Pseudocnus echinatus
Macromolecule	hemolytic lectin CEL-III (protein)
Unique Ligands	BTB, CA, CL, MG

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1XA3 \| pdb_00001xa3	Download File View File

Crystal structure of CaiB, a type III CoA transferase in carnitine metabolism

Stenmark, P., Gurmu, D., Nordlund, P., Structural Proteomics in Europe (SPINE)

(2004) Biochemistry 43: 13996-14003

Released	2004-11-16
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Escherichia coli
Macromolecule	Crotonobetainyl-CoA:carnitine CoA-transferase (protein)
Unique Ligands	BTB, SO4

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1XA4 \| pdb_00001xa4	Download File View File

Crystal structure of CaiB, a type III CoA transferase in carnitine metabolism

Stenmark, P., Gurmu, D., Nordlund, P.

(2004) Biochemistry 43: 13996-14003

Released	2004-11-16
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli
Macromolecule	Crotonobetainyl-CoA:carnitine CoA-transferase (protein)
Unique Ligands	BTB, COA, SO4

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2BIB \| pdb_00002bib	Download File View File

Crystal structure of the complete modular teichioic acid phosphorylcholine esterase Pce (CbpE) from Streptococcus pneumoniae

Hermoso, J.A., Lagartera, L., Gonzalez, A., Garcia, P., Martinez-Ripoll, M., Garcia, J.L., Menendez, M.

(2005) Nat Struct Mol Biol 12: 533

Released	2005-05-09
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Streptococcus pneumoniae
Macromolecule	TEICHOIC ACID PHOSPHORYLCHOLINE ESTERASE/ CHOLINE BINDING PROTEIN (protein)
Unique Ligands	BTB, CA, PC, ZN

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2C59 \| pdb_00002c59	Download File View File

gdp-mannose-3', 5' -epimerase (arabidopsis thaliana), with gdp-alpha-d-mannose and gdp-beta-l-galactose bound in the active site.

Major, L.L., Wolucka, B.A., Naismith, J.H.

(2005) J Am Chem Soc 127: 18309

Released	2005-11-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Arabidopsis thaliana
Macromolecule	GDP-MANNOSE-3', 5'-EPIMERASE (protein)
Unique Ligands	BTB, FMT, GDC, GDD, NAD

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2C5A \| pdb_00002c5a	Download File View File

GDP-mannose-3', 5' -epimerase (Arabidopsis thaliana),Y174F, with GDP-beta-L-galactose bound in the active site

Major, L.L., Wolucka, B.A., Naismith, J.H.

(2005) J Am Chem Soc 127: 18309

Released	2005-11-14
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Arabidopsis thaliana
Macromolecule	GDP-MANNOSE-3', 5'-EPIMERASE (protein)
Unique Ligands	BTB, FMT, GDC, NAD

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2E3V \| pdb_00002e3v	Download File View File

Crystal structure of the first fibronectin type III domain of neural cell adhesion molecule splicing isoform from human muscle culture lambda-4.4

Nishino, A., Saijo, S., Kishishita, S., Chen, L., Liu, Z.J., Wang, B.C., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-06-05
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	Neural cell adhesion molecule 1, 140 kDa isoform (protein)
Unique Ligands	BTB, EDO, PEG, PGE

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2EI5 \| pdb_00002ei5	Download File View File

Crystal Structure of Hypothetical protein(TTHA0061) from Thermus thermophilus

Niwa, H., Kumarevel, T.S., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-09-18
Method	X-RAY DIFFRACTION 1.88 Å
Organisms	Thermus thermophilus
Macromolecule	Hypothetical protein TTHA0061 (protein)
Unique Ligands	BTB

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2F07 \| pdb_00002f07	Download File View File

Crystal Structure of YvdT from Bacillus subtilis

Su, X.-D., Yu, Y.-M., Nan, J.

To be published

Released	2006-11-21
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168
Macromolecule	YvdT (protein)
Unique Ligands	BTB

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2HVR \| pdb_00002hvr	Download File View File

Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex containing a 3'-deoxyribonucleotide at the nick

Nandakumar, J., Lima, C.D.

(2006) Cell 127: 71-84

Released	2006-10-17
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Tequatrovirus T4
Macromolecule	T4 RNA ligase 2 (protein) 5'-D(APTPTPCPCPGPAPTPAPGPTPGPGPGPGPTPCPGPCPAPAPTPTPG)-3' (nucleic acid) 5'-D(CPAPAPTPTPGPCPGPAPC)-R(P(OMC)PC)-3' (hybrid) 5'-R(PA)-D(PCPAPCPTPAPTPCPGPGPAPAP*T)-3' (hybrid)
Unique Ligands	BTB

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2HVS \| pdb_00002hvs	Download File View File

Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex containing a 2'-deoxyribonucleotide at the nick

Nandakumar, J., Lima, C.D.

(2006) Cell 127: 71-84

Released	2006-10-17
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Tequatrovirus T4
Macromolecule	T4 RNA Ligase 2 (protein) 5'-D(APTPTPCPCPGPAPTPAPGPTPGPGPGPGPTPCPGPCPAPAPTPTPG)-3' (nucleic acid) 5'-D(PCPAPCPTPAPTPCPGPGPAPAPT)-3' (nucleic acid) 5'-D(CPAPAPTPTPGPCPGPAPC)-R(P(OMC)PC)-3' (hybrid)
Unique Ligands	AMP, BTB

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2I3A \| pdb_00002i3a	Download File View File

Crystal structure of N-Acetyl-gamma-Glutamyl-Phosphate Reductase (Rv1652) from Mycobacterium tuberculosis

Cherney, L.T., Cherney, M.M., Garen, C.R., Moraidin, F., James, M.N.G., Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)

(2007) J Mol Biology 367: 1357-1369

Released	2006-08-29
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	N-acetyl-gamma-glutamyl-phosphate reductase (protein)
Unique Ligands	BTB

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2I3G \| pdb_00002i3g	Download File View File

Crystal structure of N-Acetyl-gamma-Glutamyl-Phosphate Reductase (Rv1652) from Mycobacterium tuberculosis in complex with NADP+.

Cherney, L.T., Cherney, M.M., Garen, C.R., Moraidin, F., James, M.N.G., Mycobacterium Tuberculosis Structural Proteomics Project (XMTB), TB Structural Genomics Consortium (TBSGC)

(2007) J Mol Biology 367: 1357-1369

Released	2006-09-05
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	N-acetyl-gamma-glutamyl-phosphate reductase (protein)
Unique Ligands	BTB, NAP

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2I3H \| pdb_00002i3h	Download File View File

Structure of an ML-IAP/XIAP chimera bound to a 4-mer peptide (AVPW)

Fairbrother, W.J., Franklin, M.C.

(2006) ACS Chem Biol 1: 525-533

Released	2006-09-19
Method	X-RAY DIFFRACTION 1.62 Å
Organisms	Homo sapiens
Macromolecule	AVPW peptide (protein) Baculoviral IAP repeat-containing protein 7 (protein)
Unique Ligands	BTB, EDO, LI, ZN

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2I3I \| pdb_00002i3i	Download File View File

Structure of an ML-IAP/XIAP chimera bound to a peptidomimetic

Fairbrother, W.J., Franklin, M.C.

(2006) ACS Chem Biol 1: 525-533

Released	2006-09-19
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Baculoviral IAP repeat-containing protein 7 (protein)
Unique Ligands	618, BTB, EDO, LI, ZN

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2IC5 \| pdb_00002ic5	Download File View File

Crystal structure of human RAC3 grown in the presence of Gpp(NH)p.

Ugochukwu, E., Yang, X., Zao, Y., Elkins, J., Gileadi, C., Burgess, N., Colebrook, S., Gileadi, O., Fedorov, O., Bunkoczi, G., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A., von Delft, F., Doyle, D., Structural Genomics Consortium (SGC)

To be published

Released	2006-10-10
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Ras-related C3 botulinum toxin substrate 3 (protein)
Unique Ligands	BTB, CL, GDP, GNP, MG