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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Caaveiro, J.M.M."

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Search Summary

This query matches 1,318 Structures.

Refinements

Structure Determination Methodology

experimental (1,318)

Scientific Name of Source Organism

	Homo sapiens (528)
	synthetic construct (210)
	Human immunodeficiency virus 1 (133)
	Hirudo medicinalis (75)
	Saccharomyces cerevisiae S288C (75)
	Severe acute respiratory syndrome coronavirus 2 (73)
	Bos taurus (49)
	Cryphonectria parasitica (32)
	Gallus gallus (29)
	Lysobacter enzymogenes (29)

More...

Taxonomy

	Eukaryota (806)
	Riboviria (335)
	other sequences (210)
	Bacteria (167)
	Riboviria (RNA viruses and viroids) (24)
	unclassified sequences (16)
	Eukaryota (eukaryotes) (12)
	Duplodnaviria (10)
	Archaea (5)

Experimental Method

	X-RAY DIFFRACTION (1,252)
	ELECTRON MICROSCOPY (53)
	SOLUTION NMR (9)
	NEUTRON DIFFRACTION (6)
	SOLID-STATE NMR (1)

Polymer Entity Type

	Protein (1,317)
	DNA (27)
	RNA (15)

Refinement Resolution (Å)

	0.5 - 1.0 (11)
	1.0 - 1.5 (144)
	1.5 - 2.0 (478)
	2.0 - 2.5 (329)
	2.5 - 3.0 (237)
	3.0 - 3.5 (80)
	3.5 - 4.0 (29)
	4.0 - 4.5 (1)
	> 4.5 (1)

Release Date

	1975 - 1979 (4)
	1985 - 1989 (7)
	1990 - 1994 (78)
	1995 - 1999 (99)
	2000 - 2004 (110)
	2005 - 2009 (202)
	2010 - 2014 (385)
	2015 - 2019 (234)
	2020 - 2024 (187)
	2025 - 2029 (12)

Enzyme Classification Name

	Hydrolases (1,055)
	Transferases (57)
	Oxidoreductases (6)
	Isomerases (11)
	Ligases (11)
	Translocases (5)

Membrane Protein Annotation

	PDBTM (24)
	OPM (22)
	mpstruc (16)
	MemProtMD (17)

Symmetry Type

	Asymmetric (813)
	Cyclic (534)
	Dihedral (30)
	Helical (4)
	Tetrahedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (203)
	All beta proteins (518)
	Artifacts (122)
	Alpha and beta proteins (a/b) (70)
	Small proteins (37)
	All alpha proteins (26)
	Coiled coil proteins (2)
	Membrane and cell surface proteins and peptides (4)

AllSelected

1 to 25 of 1,318 Structures

Page 1 of 53

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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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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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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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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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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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1AAQ \| pdb_00001aaq	Download File View File

HYDROXYETHYLENE ISOSTERE INHIBITORS OF HUMAN IMMUNODEFICIENCY VIRUS-1 PROTEASE: STRUCTURE-ACTIVITY ANALYSIS USING ENZYME KINETICS, X-RAY CRYSTALLOGRAPHY, AND INFECTED T-CELL ASSAYS

Lewis, M.

(1992) Biochemistry 31: 6646-6659

Released	1994-06-22
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Human immunodeficiency virus 1
Macromolecule	HIV-1 PROTEASE (protein)
Unique Ligands	PSI

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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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1AF0 \| pdb_00001af0	Download File View File

SERRATIA PROTEASE IN COMPLEX WITH INHIBITOR

Baumann, U.

To be published

Released	1998-03-25
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Serratia marcescens
Macromolecule	SERRATIA PROTEASE (protein)
Unique Ligands	0Z9, CA, ZN

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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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1ARC \| pdb_00001arc	Download File View File

THE PRIMARY STRUCTURE AND STRUCTURAL CHARACTERISTICS OF ACHROMOBACTER LYTICUS PROTEASE I, A LYSINE-SPECIFIC SERINE PROTEASE

Kitagawa, Y., Katsube, Y.

(1989) J Biological Chem 264: 3832-3839

Released	1993-10-31
Method	X-RAY DIFFRACTION 2 Å
Organisms	Achromobacter lyticus
Macromolecule	ACHROMOBACTER PROTEASE I (protein)
Unique Ligands	TCK

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1AU8 \| pdb_00001au8	Download File View File

HUMAN CATHEPSIN G

Medrano, F.J., Bode, W., Banbula, A., Potempa, J.

To be published

Released	1998-10-14
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	CATHEPSIN G (protein)
Unique Ligands	0H8

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1AUT \| pdb_00001aut	Download File View File

Human activated protein C

Mather, T., Oganessyan, V., Hof, P., Bode, W., Huber, R., Foundling, S., Esmon, C.

(1996) EMBO J 15: 6822-6831

Released	1997-08-20
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	ACTIVATED PROTEIN C (protein)
Unique Ligands	0G6

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1AY6 \| pdb_00001ay6	Download File View File

THROMBIN INHIBITOR FROM THEONALLA, CYCLOTHEANAMIDE-BASED MACROCYCLIC TRIPEPTIDE MOTIF

Ganesh, V., Maryanoff, B.E., Tulinsky, A.

(1996) Bioorg Med Chem Lett 6: 2947-2952

Released	1998-03-18
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	HIRUGEN (protein) THROMBIN HEAVY CHAIN (protein) THROMBIN LIGHT CHAIN (protein)
Unique Ligands	1ZV

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1B11 \| pdb_00001b11	Download File View File

STRUCTURE OF FELINE IMMUNODEFICIENCY VIRUS PROTEASE COMPLEXED WITH TL-3-093

Gustchina, A., Li, M., Wlodawer, A.

(2000) Proteins 38: 29-40

Released	1998-12-02
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Feline immunodeficiency virus
Macromolecule	PROTEIN (Feline Immunodeficiency Virus PROTEASE) (protein)
Unique Ligands	3TL, SO4

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1B6J \| pdb_00001b6j	Download File View File

HIV-1 PROTEASE COMPLEXED WITH MACROCYCLIC PEPTIDOMIMETIC INHIBITOR 1

Martin, J.L., Begun, J., Schindeler, A., Wickramasinghe, W.A., Alewood, D., Alewood, P.F., Bergman, D.A., Brinkworth, R.I., Abbenante, G., March, D.R., Reid, R.C., Fairlie, D.P.

(1999) Biochemistry 38: 7978-7988

Released	2000-01-07
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Human immunodeficiency virus 1
Macromolecule	CYCLIC PEPTIDE INHIBITOR (protein) RETROPEPSIN (protein)
Unique Ligands	SO4

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1B6M \| pdb_00001b6m	Download File View File

HIV-1 PROTEASE COMPLEXED WITH MACROCYCLIC PEPTIDOMIMETIC INHIBITOR 6

Martin, J.L., Begun, J., Schindeler, A., Wickramasinghe, W.A., Alewood, D., Alewood, P.F., Bergman, D.A., Brinkworth, R.I., Abbenante, G., March, D.R., Reid, R.C., Fairlie, D.P.

(1999) Biochemistry 38: 7978-7988

Released	2000-01-07
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Human immunodeficiency virus 1
Macromolecule	RETROPEPSIN (protein)
Unique Ligands	PI6, SO4

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1BA8 \| pdb_00001ba8	Download File View File

THROMBIN INHIBITOR WITH A RIGID TRIPEPTIDYL ALDEHYDES

Krishnan, R., Zhang, E., Hakansson, K., Arni, R.K., Tulinsky, A., Lim-Wilby, M.S.L., Levy, O.E., Semple, J.E., Brunck, T.K.

(1998) Biochemistry 37: 12094-12103

Released	1999-04-27
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	HIRUGEN (protein) THROMBIN (protein)
Unique Ligands	0IT, NAG

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1BAI \| pdb_00001bai	Download File View File

Crystal structure of Rous sarcoma virus protease in complex with inhibitor

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 2.4 Å
Organisms	Rous sarcoma virus
Macromolecule	PROTEASE (protein)
Unique Ligands	0Q4

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1BB0 \| pdb_00001bb0	Download File View File

THROMBIN INHIBITORS WITH RIGID TRIPEPTIDYL ALDEHYDES

Krishnan, R., Zhang, E., Hakansson, K., Arni, R.K., Tulinsky, A., Lim-Wilby, M.S.L., Levy, O.E., Semple, J.E., Brunck, T.K.

(1998) Biochemistry 37: 12094-12103

Released	1999-04-27
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	HIRUGEN (protein) THROMBIN (protein)
Unique Ligands	0IV, NA

1 to 25 of 1,318 Structures

Page 1 of 53

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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

1A46 | pdb_00001a46

1A4W | pdb_00001a4w

1A5G | pdb_00001a5g

1A5I | pdb_00001a5i

1A61 | pdb_00001a61

1A85 | pdb_00001a85

1A86 | pdb_00001a86

1A8G | pdb_00001a8g

1A8K | pdb_00001a8k

1A94 | pdb_00001a94

1AAQ | pdb_00001aaq

1ABJ | pdb_00001abj

1AF0 | pdb_00001af0

1AFQ | pdb_00001afq

1ARC | pdb_00001arc

1AU8 | pdb_00001au8

1AUT | pdb_00001aut

1AY6 | pdb_00001ay6

1B11 | pdb_00001b11

1B6J | pdb_00001b6j

1B6M | pdb_00001b6m

1BA8 | pdb_00001ba8

1BAI | pdb_00001bai

1BB0 | pdb_00001bb0