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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 = 3.4.21

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Search Summary

This query matches 4,770 Structures.

Refinements

Structure Determination Methodology

experimental (4,770)

Scientific Name of Source Organism

	Homo sapiens (1,936)
	Bos taurus (858)
	Hirudo medicinalis (304)
	Parengyodontium album (254)
	synthetic construct (217)
	Sus scrofa (202)
	Zika virus (197)
	Escherichia coli (169)
	Escherichia coli K-12 (89)
	Mus musculus (78)

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Taxonomy

	Eukaryota (3,549)
	Bacteria (949)
	Riboviria (463)
	other sequences (224)
	Eukaryota (eukaryotes) (57)
	Archaea (40)
	Duplodnaviria (33)
	unclassified sequences (7)
	Varidnaviria (6)
	Riboviria (RNA viruses and viroids) (5)

Experimental Method

	X-RAY DIFFRACTION (4,342)
	ELECTRON MICROSCOPY (287)
	SOLUTION NMR (78)
	ELECTRON CRYSTALLOGRAPHY (56)
	NEUTRON DIFFRACTION (17)

Polymer Entity Type

	Protein (4,770)
	DNA (43)
	RNA (19)

Refinement Resolution (Å)

	0.5 - 1.0 (64)
	1.0 - 1.5 (674)
	1.5 - 2.0 (1,662)
	2.0 - 2.5 (1,247)
	2.5 - 3.0 (581)
	3.0 - 3.5 (270)
	3.5 - 4.0 (88)
	4.0 - 4.5 (42)
	> 4.5 (72)

Release Date

	1975 - 1979 (7)
	1980 - 1984 (21)
	1985 - 1989 (23)
	1990 - 1994 (166)
	1995 - 1999 (324)
	2000 - 2004 (611)
	2005 - 2009 (759)
	2010 - 2014 (802)
	2015 - 2019 (761)
	2020 - 2024 (1,161)

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Enzyme Classification Name

	Hydrolases (4,770)
	Transferases (101)
	Oxidoreductases (26)
	Lyases (7)
	Isomerases (3)
	Ligases (1)

Membrane Protein Annotation

	PDBTM (89)
	OPM (76)
	MemProtMD (74)
	mpstruc (64)

Symmetry Type

	Asymmetric (4,169)
	Cyclic (538)
	Dihedral (198)
	Icosahedral (34)
	Helical (21)
	Tetrahedral (8)
	Octahedral (7)

SCOP Classification

	All beta proteins (2,164)
	Alpha and beta proteins (a/b) (687)
	Small proteins (592)
	Artifacts (177)
	Alpha and beta proteins (a+b) (91)
	Multi-domain proteins (alpha and beta) (41)
	Membrane and cell surface proteins and peptides (34)
	All alpha proteins (15)
	Low resolution protein structures (1)
	Coiled coil proteins (2)

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AllSelected

1 to 25 of 4,770 Structures

Page 1 of 191

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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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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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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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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)

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1ABJ \| pdb_00001abj	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 2.4 Å
Organisms	Homo sapiens
Macromolecule	ALPHA-THROMBIN (LARGE SUBUNIT) (protein) ALPHA-THROMBIN (SMALL SUBUNIT) (protein)
Unique Ligands	0G6

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1ACB \| pdb_00001acb	Download File View File

CRYSTAL AND MOLECULAR STRUCTURE OF THE BOVINE ALPHA-CHYMOTRYPSIN-EGLIN C COMPLEX AT 2.0 ANGSTROMS RESOLUTION

Bolognesi, M., Frigerio, F., Coda, A., Pugliese, L., Lionetti, C., Menegatti, E., Amiconi, G., Schnebli, H.P., Ascenzi, P.

(1992) J Mol Biology 225: 107-123

Released	1993-10-31
Method	X-RAY DIFFRACTION 2 Å
Organisms	Bos taurus Hirudo medicinalis
Macromolecule	ALPHA-CHYMOTRYPSIN (protein) Eglin C (protein)

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1AD8 \| pdb_00001ad8	Download File View File

COMPLEX OF THROMBIN WITH AND INHIBITOR CONTAINING A NOVEL P1 MOIETY

Schreuder, H., Tardif, C., Malikayil, J.A.

(1997) Biochemistry 36: 1034-1040

Released	1997-11-12
Method	X-RAY DIFFRACTION 2 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	HIRUDIN (53-65) PEPTIDE (protein) THROMBIN (LARGE SUBUNIT) (protein) THROMBIN (SMALL SUBUNIT) (protein)
Unique Ligands	MDL, NA

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1AE8 \| pdb_00001ae8	Download File View File

HUMAN ALPHA-THROMBIN INHIBITION BY EOC-D-PHE-PRO-AZALYS-ONP

De Simone, G., Balliano, G., Milla, P., Gallina, C., Giordano, C., Tarricone, C., Rizzi, M., Bolognesi, M., Ascenzi, P.

(1997) J Mol Biology 269: 558-569

Released	1997-12-03
Method	X-RAY DIFFRACTION 2 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	ALPHA-THROMBIN (LARGE SUBUNIT) (protein) ALPHA-THROMBIN (SMALL SUBUNIT) (protein) HIRUGEN (protein)
Unique Ligands	AZL, NAG

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1AF4 \| pdb_00001af4	Download File View File

CRYSTAL STRUCTURE OF SUBTILISIN CARLSBERG IN ANHYDROUS DIOXANE

Schmitke, J.L., Stern, L.J., Klibanov, A.M.

(1997) Proc Natl Acad Sci U S A 94: 4250-4255

Released	1997-06-16
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Bacillus licheniformis
Macromolecule	SUBTILISIN CARLSBERG (protein)
Unique Ligands	CA, DIO

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1AFE \| pdb_00001afe	Download File View File

HUMAN ALPHA-THROMBIN INHIBITION BY CBZ-PRO-AZALYS-ONP

De Simone, G., Balliano, G., Milla, P., Gallina, C., Giordano, C., Tarricone, C., Rizzi, M., Bolognesi, M., Ascenzi, P.

(1997) J Mol Biology 269: 558-569

Released	1997-12-03
Method	X-RAY DIFFRACTION 2 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	ALPHA-THROMBIN (LARGE SUBUNIT) (protein) ALPHA-THROMBIN (SMALL SUBUNIT) (protein) HIRUGEN (protein)
Unique Ligands	ALZ, NAG

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1AFQ \| pdb_00001afq	Download File View File

CRYSTAL STRUCTURE OF BOVINE GAMMA-CHYMOTRYPSIN COMPLEXED WITH A SYNTHETIC INHIBITOR

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

(1998) Eur J Biochem 255: 12-23

Released	1997-09-17
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bos taurus
Macromolecule	BOVINE GAMMA-CHYMOTRYPSIN (protein)
Unique Ligands	0FG, SO4

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1AGJ \| pdb_00001agj	Download File View File

EPIDERMOLYTIC TOXIN A FROM STAPHYLOCOCCUS AUREUS

Cavarelli, J.

(1997) Structure 5: 813-824

Released	1997-09-26
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Staphylococcus aureus
Macromolecule	EPIDERMOLYTIC TOXIN A (protein)

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1AH2 \| pdb_00001ah2	Download File View File

SERINE PROTEASE PB92 FROM BACILLUS ALCALOPHILUS, NMR, 18 STRUCTURES

Boelens, R., Schipper, D., Martin, J.R., Karimi-Nejad, Y., Mulder, F., Zwan, J.V.D., Mariani, M.

(1997) Structure 5: 521-532

Released	1998-04-15
Method	SOLUTION NMR
Organisms	Alkalihalobacillus alcalophilus
Macromolecule	SERINE PROTEASE PB92 (protein)

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1AHT \| pdb_00001aht	Download File View File

CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN COMPLEXED WITH HIRUGEN AND P-AMIDINOPHENYLPYRUVATE AT 1.6 ANGSTROMS RESOLUTION

Chen, Z.

(1995) Arch Biochem Biophys 322: 198-203

Released	1996-03-17
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	ALPHA-THROMBIN (LARGE SUBUNIT) (protein) ALPHA-THROMBIN (SMALL SUBUNIT) (protein) HIRUGEN (protein)
Unique Ligands	APA

1 to 25 of 4,770 Structures

Page 1 of 191

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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

1A2C | pdb_00001a2c

1A2Q | pdb_00001a2q

1A3B | pdb_00001a3b

1A3E | pdb_00001a3e

1A46 | pdb_00001a46

1A4W | pdb_00001a4w

1A5G | pdb_00001a5g

1A5H | pdb_00001a5h

1A5I | pdb_00001a5i

1A61 | pdb_00001a61

1AB9 | pdb_00001ab9

1ABI | pdb_00001abi

1ABJ | pdb_00001abj

1ACB | pdb_00001acb

1AD8 | pdb_00001ad8

1AE8 | pdb_00001ae8

1AF4 | pdb_00001af4

1AFE | pdb_00001afe

1AFQ | pdb_00001afq

1AGJ | pdb_00001agj

1AH2 | pdb_00001ah2

1AHT | pdb_00001aht