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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Enzyme Classification Number = 3.4

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Search Summary

This query matches 16,420 Structures.

Refinements

Structure Determination Methodology

experimental (16,420)

Scientific Name of Source Organism

	Homo sapiens (5,623)
	Severe acute respiratory syndrome coronavirus 2 (2,528)
	Bos taurus (959)
	Cryphonectria parasitica (849)
	synthetic construct (576)
	Human immunodeficiency virus 1 (386)
	Saccharomyces cerevisiae S288C (341)
	Escherichia coli (316)
	Hirudo medicinalis (306)
	Coxsackievirus A16 (301)

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Taxonomy

	Eukaryota (9,593)
	Riboviria (4,639)
	Bacteria (2,834)
	other sequences (583)
	Archaea (176)
	Eukaryota (eukaryotes) (91)
	Duplodnaviria (89)
	Riboviria (RNA viruses and viroids) (51)
	Varidnaviria (26)
	unclassified sequences (26)

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Experimental Method

	X-RAY DIFFRACTION (14,781)
	ELECTRON MICROSCOPY (1,316)
	SOLUTION NMR (243)
	ELECTRON CRYSTALLOGRAPHY (71)
	NEUTRON DIFFRACTION (29)
	SOLID-STATE NMR (2)
	SOLUTION SCATTERING (1)

Polymer Entity Type

	Protein (16,420)
	RNA (109)
	DNA (102)
	NA-hybrid (1)

Refinement Resolution (Å)

	0.5 - 1.0 (152)
	1.0 - 1.5 (2,755)
	1.5 - 2.0 (5,492)
	2.0 - 2.5 (3,786)
	2.5 - 3.0 (2,253)
	3.0 - 3.5 (1,030)
	3.5 - 4.0 (373)
	4.0 - 4.5 (141)
	> 4.5 (210)

Release Date

	1975 - 1979 (13)
	1980 - 1984 (28)
	1985 - 1989 (35)
	1990 - 1994 (256)
	1995 - 1999 (616)
	2000 - 2004 (1,215)
	2005 - 2009 (2,190)
	2010 - 2014 (2,590)
	2015 - 2019 (3,146)
	2020 - 2024 (5,797)

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Enzyme Classification Name

	Hydrolases (16,420)
	Transferases (647)
	Translocases (26)
	Oxidoreductases (61)
	Lyases (62)
	Ligases (35)
	Isomerases (14)

Membrane Protein Annotation

	PDBTM (208)
	mpstruc (177)
	OPM (157)
	MemProtMD (145)

Symmetry Type

	Asymmetric (11,523)
	Cyclic (4,703)
	Dihedral (535)
	Icosahedral (153)
	Helical (40)
	Tetrahedral (40)
	Octahedral (7)

SCOP Classification

	Alpha and beta proteins (a+b) (2,210)
	All beta proteins (5,073)
	Alpha and beta proteins (a/b) (1,608)
	Artifacts (1,150)
	Small proteins (641)
	All alpha proteins (269)
	Multi-domain proteins (alpha and beta) (203)
	Membrane and cell surface proteins and peptides (37)
	Coiled coil proteins (20)
	Low resolution protein structures (1)

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AllSelected

1 to 25 of 16,420 Structures

Page 1 of 657

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1A0H \| pdb_00001a0h	Download File View File

THE X-RAY CRYSTAL STRUCTURE OF PPACK-MEIZOTHROMBIN DESF1: KRINGLE/THROMBIN AND CARBOHYDRATE/KRINGLE/THROMBIN INTERACTIONS AND LOCATION OF THE LINKER CHAIN

Martin, P.D., Malkowski, M.G., Box, J., Esmon, C.T., Edwards, B.F.P.

(1997) Structure 5: 1681-1693

Released	1998-06-17
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Bos taurus
Macromolecule	MEIZOTHROMBIN (protein)
Unique Ligands	0G6
Unique branched monosaccharides	NAG

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1A0J \| pdb_00001a0j	Download File View File

CRYSTAL STRUCTURE OF A NON-PSYCHROPHILIC TRYPSIN FROM A COLD-ADAPTED FISH SPECIES.

Schroeder, H.-K., Willassen, N.P., Smalaas, A.O.

(1998) Acta Crystallogr D Biol Crystallogr 54: 780-798

Released	1999-01-13
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Salmo salar
Macromolecule	TRYPSIN (protein)
Unique Ligands	BEN, CA, SO4

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1A0L \| pdb_00001a0l	Download File View File

HUMAN BETA-TRYPTASE: A RING-LIKE TETRAMER WITH ACTIVE SITES FACING A CENTRAL PORE

Pereira, P.J.B., Bergner, A., Macedo-Ribeiro, S., Huber, R., Matschiner, G., Fritz, H., Sommerhoff, C.P., Bode, W.

(1998) Nature 392: 306-311

Released	1999-03-23
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	BETA-TRYPTASE (protein)
Unique Ligands	APA

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1A16 \| pdb_00001a16	Download File View File

AMINOPEPTIDASE P FROM E. COLI WITH THE INHIBITOR PRO-LEU

Wilce, M.C., Bond, C.S., Lilley, P.E., Dixon, N.E., Freeman, H.C., Guss, J.M.

(1998) Proc Natl Acad Sci U S A 95: 3472-3477

Released	1999-04-06
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Escherichia coli
Macromolecule	AMINOPEPTIDASE P (protein)
Unique Ligands	LEU, MN, PRO

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1A2C \| pdb_00001a2c	Download File View File

Structure of thrombin inhibited by AERUGINOSIN298-A from a BLUE-GREEN ALGA

Rios-Steiner, J.L., Murakami, M., Tulinsky, A.

(1998) J Am Chem Soc 120: 597

Released	1998-07-01
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Hirudo medicinalis Homo sapiens Microcystis aeruginosa
Macromolecule	Aeruginosin 298-A (protein) Hirudin variant-2 (protein) Thrombin heavy chain (protein) Thrombin light chain (protein)
Unique Ligands	NA

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1A2Q \| pdb_00001a2q	Download File View File

SUBTILISIN BPN' MUTANT 7186

Gilliland, G.L., Whitlow, M., Howard, A.J.

(1989) Biochemistry 28: 7205-7213

Released	1998-04-29
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bacillus amyloliquefaciens
Macromolecule	SUBTILISIN BPN' (protein)
Unique Ligands	ACN, CA

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1A2Z \| pdb_00001a2z	Download File View File

PYRROLIDONE CARBOXYL PEPTIDASE FROM THERMOCOCCUS LITORALIS

Singleton, M.R., Isupov, M.N., Littlechild, J.A.

(1999) Structure 7: 237-244

Released	1998-07-15
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	Thermococcus litoralis
Macromolecule	PYRROLIDONE CARBOXYL PEPTIDASE (protein)
Unique Ligands	SO4

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1A30 \| pdb_00001a30	Download File View File

HIV-1 PROTEASE COMPLEXED WITH A TRIPEPTIDE INHIBITOR

Louis, J.M., Dyda, F., Nashed, N.T., Kimmel, A.R., Davies, D.R.

(1998) Biochemistry 37: 2105-2110

Released	1998-04-29
Method	X-RAY DIFFRACTION 2 Å
Organisms	Human immunodeficiency virus 1
Macromolecule	HIV-1 PROTEASE (protein) TRIPEPTIDE GLU-ASP-LEU (protein)

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1A3B \| pdb_00001a3b	Download File View File

COMPLEX OF HUMAN ALPHA-THROMBIN WITH THE BIFUNCTIONAL BORONATE INHIBITOR BOROLOG1

Skordalakes, E., Elgendy, S., Dodson, G., Goodwin, C.A., Green, D., Scully, M.F., Freyssinet, J.H., Kakkar, V.V., Deadman, J.

(1998) Biochemistry 37: 14420-14427

Released	1998-06-03
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	ALPHA-THROMBIN (LARGE SUBUNIT) (protein) ALPHA-THROMBIN (SMALL SUBUNIT) (protein) Hirudin (protein)
Unique Ligands	T29

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1A3E \| pdb_00001a3e	Download File View File

COMPLEX OF HUMAN ALPHA-THROMBIN WITH THE BIFUNCTIONAL BORONATE INHIBITOR BOROLOG2

Skordalakes, E., Elgendy, S., Goodwin, C.A., Green, D., Scullly, M.F., Kakkar, V.V., Freyssinet, J.M., Dodson, G., Deadman, J.

(1998) Biochemistry 37: 14420-14427

Released	1998-06-03
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	ALPHA-THROMBIN (LARGE SUBUNIT) (protein) ALPHA-THROMBIN (SMALL SUBUNIT) (protein) Hirudin (protein)
Unique Ligands	T16

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1A46 \| pdb_00001a46	Download File View File

THROMBIN COMPLEXED WITH HIRUGEN AND A BETA-STRAND MIMETIC INHIBITOR

St Charles, R., Matthews, J.H., Zhang, E., Tulinsky, A., Kahn, M.

(1999) J Med Chem 42: 1376-1383

Released	1998-05-27
Method	X-RAY DIFFRACTION 2.12 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	ALPHA-THROMBIN (LARGE SUBUNIT) (protein) ALPHA-THROMBIN (SMALL SUBUNIT) (protein) HIRUGEN (protein)
Unique Ligands	00K, NA

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1A4W \| pdb_00001a4w	Download File View File

CRYSTAL STRUCTURES OF THROMBIN WITH THIAZOLE-CONTAINING INHIBITORS: PROBES OF THE S1' BINDING SITE

Matthews, J.H., Krishnan, R., Costanzo, M.J., Maryanoff, B.E., Tulinsky, A.

(1996) Biophys J 71: 2830-2839

Released	1998-04-29
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	ALPHA-THROMBIN (LARGE SUBUNIT) (protein) ALPHA-THROMBIN (SMALL SUBUNIT) (protein) HIRUGEN (protein)
Unique Ligands	NA, QWE

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1A5G \| pdb_00001a5g	Download File View File

HUMAN THROMBIN COMPLEXED WITH NOVEL SYNTHETIC PEPTIDE MIMETIC INHIBITOR AND HIRUGEN

St Charles, R., Tulinsky, A., Kahn, M.

(1999) J Med Chem 42: 1376-1383

Released	1998-05-27
Method	X-RAY DIFFRACTION 2.06 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	ALPHA-THROMBIN (LARGE SUBUNIT) (protein) ALPHA-THROMBIN (SMALL SUBUNIT) (protein) HIRUGEN (protein)
Unique Ligands	00L, NA

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1A5H \| pdb_00001a5h	Download File View File

CATALYTIC DOMAIN OF HUMAN TWO-CHAIN TISSUE PLASMINOGEN ACTIVATOR COMPLEX OF A BIS-BENZAMIDINE

Renatus, M., Bode, W., Stubbs, M.T.

(1997) J Biological Chem 272: 21713-21719

Released	1999-04-20
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens
Macromolecule	TISSUE PLASMINOGEN ACTIVATOR (protein)
Unique Ligands	BBA

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1A5I \| pdb_00001a5i	Download File View File

CATALYTIC DOMAIN OF VAMPIRE BAT (DESMODUS ROTUNDUS) SALIVA PLASMINOGEN ACTIVATOR IN COMPLEX WITH EGR-CMK (GLU-GLY-ARG CHLOROMETHYL KETONE)

Renatus, M., Stubbs, M.T., Bode, W.

(1997) Biochemistry 36: 13483-13493

Released	1999-03-23
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Desmodus rotundus
Macromolecule	PLASMINOGEN ACTIVATOR (protein)
Unique Ligands	0GJ

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1A61 \| pdb_00001a61	Download File View File

THROMBIN COMPLEXED WITH A BETA-MIMETIC THIAZOLE-CONTAINING INHIBITOR

St Charles, R., Matthews, J.H., Zhang, E., Tulinsky, A., Kahn, M.

(1999) J Med Chem 42: 1376-1383

Released	1998-06-17
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	ALPHA-THROMBIN (LARGE SUBUNIT) (protein) ALPHA-THROMBIN (SMALL SUBUNIT) (protein) HIRUGEN (protein)
Unique Ligands	00N, NA

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1A6R \| pdb_00001a6r	Download File View File

GAL6 (YEAST BLEOMYCIN HYDROLASE) MUTANT C73A

Joshua-Tor, L., Zheng, W., Johnston, S.A.

(1998) Cell 93: 103-109

Released	1998-10-21
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	GAL6 (protein)
Unique Ligands	SO4

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1A85 \| pdb_00001a85	Download File View File

MMP8 WITH MALONIC AND ASPARAGINE BASED INHIBITOR

Brandstetter, H., Roedern, E.G.V., Grams, F., Engh, R.A.

(1998) Protein Sci 7: 1303-1309

Released	1999-04-27
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	MMP-8 (protein)
Unique Ligands	0DY, CA, ZN

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1A86 \| pdb_00001a86	Download File View File

MMP8 WITH MALONIC AND ASPARTIC ACID BASED INHIBITOR

Brandstetter, H., Roedern, E.G.V., Grams, F., Engh, R.A.

(1998) Protein Sci 7: 1303-1309

Released	1999-05-04
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	MMP-8 (protein)
Unique Ligands	0ZB, CA, ZN

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1A8D \| pdb_00001a8d	Download File View File

TETANUS TOXIN C FRAGMENT

Knapp, M., Rupp, B.

(1998) Am Cryst Assoc ,abstr Papers (annual Meeting) 25: 90

Released	1998-10-14
Method	X-RAY DIFFRACTION 1.57 Å
Organisms	Clostridium tetani
Macromolecule	TETANUS NEUROTOXIN (protein)
Unique Ligands	AU

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1A8G \| pdb_00001a8g	Download File View File

HIV-1 PROTEASE IN COMPLEX WITH SDZ283-910

Kallen, J., Billich, A., Scholz, D., Auer, M., Kungl, A.

(1999) J Mol Biology 286: 1147-1159

Released	1998-07-15
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Human immunodeficiency virus 1
Macromolecule	HIV-1 PROTEASE (protein)
Unique Ligands	2Z4

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1A8K \| pdb_00001a8k	Download File View File

CRYSTALLOGRAPHIC ANALYSIS OF HUMAN IMMUNODEFICIENCY VIRUS 1 PROTEASE WITH AN ANALOG OF THE CONSERVED CA-P2 SUBSTRATE: INTERACTIONS WITH FREQUENTLY OCCURRING GLUTAMIC ACID RESIDUE AT P2' POSITION OF SUBSTRATES

Weber, I.T., Wu, J., Adomat, J., Harrison, R.W., Kimmel, A.R., Wondrak, E.M., Louis, J.M.

(1997) Eur J Biochem 249: 523-530

Released	1999-01-13
Method	X-RAY DIFFRACTION 2 Å
Organisms	Human immunodeficiency virus 1
Macromolecule	HIV PROTEASE (protein)
Unique Ligands	0Q4

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1A94 \| pdb_00001a94	Download File View File

STRUCTURAL BASIS FOR SPECIFICITY OF RETROVIRAL PROTEASES

Wu, J., Adomat, J.M., Ridky, T.W., Louis, J.M., Leis, J., Harrison, R.W., Weber, I.T.

(1998) Biochemistry 37: 4518-4526

Released	1999-01-13
Method	X-RAY DIFFRACTION 2 Å
Organisms	Human immunodeficiency virus 1
Macromolecule	PROTEASE (protein)
Unique Ligands	0Q4

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1AB9 \| pdb_00001ab9	Download File View File

CRYSTAL STRUCTURE OF BOVINE GAMMA-CHYMOTRYPSIN

Sugio, S., Kashima, A., Inoue, Y., Maeda, I., Nose, T., Shimohigashi, Y.

(1998) Eur J Biochem 255: 12-23

Released	1997-08-20
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Bos taurus
Macromolecule	GAMMA-CHYMOTRYPSIN (protein) PENTAPEPTIDE (TPGVY) (protein)
Unique Ligands	SO4

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1ABI \| pdb_00001abi	Download File View File

STRUCTURE OF THE HIRULOG 3-THROMBIN COMPLEX AND NATURE OF THE S' SUBSITES OF SUBSTRATES AND INHIBITORS

Qiu, X., Tulinsky, A.

(1992) Biochemistry 31: 11689-11697

Released	1994-01-31
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	ALPHA-THROMBIN (LARGE SUBUNIT) (protein) ALPHA-THROMBIN (SMALL SUBUNIT) (protein) HIRULOG 3 (protein)

1 to 25 of 16,420 Structures

Page 1 of 657

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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

1A0H | pdb_00001a0h

1A0J | pdb_00001a0j

1A0L | pdb_00001a0l

1A16 | pdb_00001a16

1A2C | pdb_00001a2c

1A2Q | pdb_00001a2q

1A2Z | pdb_00001a2z

1A30 | pdb_00001a30

1A3B | pdb_00001a3b

1A3E | pdb_00001a3e

1A46 | pdb_00001a46

1A4W | pdb_00001a4w

1A5G | pdb_00001a5g

1A5H | pdb_00001a5h

1A5I | pdb_00001a5i

1A61 | pdb_00001a61

1A6R | pdb_00001a6r

1A85 | pdb_00001a85

1A86 | pdb_00001a86

1A8D | pdb_00001a8d

1A8G | pdb_00001a8g

1A8K | pdb_00001a8k

1A94 | pdb_00001a94

1AB9 | pdb_00001ab9

1ABI | pdb_00001abi