7a0f

The Crystal Structure of Bovine Thrombin in complex with Hirudin (C22U/C39U) at 2.7 Angstroms Resolution

Method: X-RAY DIFFRACTION D_max: 68.0 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Prothrombin

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain HHH； UniProt 367–625 Chain LLL； UniProt 318–366	Not recorded	Hirudin variant-1 × 1 （P01050） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.7；297 K；38% PEG 4000, 0.1 M sodium phosphate (pH= 4.7), 0.3 M NaCl	Resolution 2.70 Å R-free 0.253

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 7A0F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A0H THE X-RAY CRYSTAL STRUCTURE OF PPACK-MEIZOTHROMBIN DESF1: KRINGLE/THROMBIN AND CARBOHYDRATE/KRINGLE/THROMBIN INTERACTIONS AND LOCATION OF THE LINKER CHAIN Deposited 1997-11-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 208–366（159 aa） Fragment：F2/THROMBIN DOMAIN Chain B 367–625（259 aa） Fragment：F2/THROMBIN DOMAIN Chain D 208–366（159 aa） Fragment：F2/THROMBIN DOMAIN Chain E 367–625（259 aa） Fragment：F2/THROMBIN DOMAIN	Not recorded	0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；17 MG/ML PROTEIN, 2% PEG4000, .25 M AMMONIUM PHOSPHATE, PH 8.0, 33% SATURATED AMMONIUM SULFATE	Resolution 3.20 Å R-free 0.242
1AVG THROMBIN INHIBITOR FROM TRIATOMA PALLIDIPENNIS Deposited 1997-09-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 367–625（259 aa） Chain L 326–366（41 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；50 MM NA ACETATE, PH 4.6, 100 MM (NH4)2SO4, 16 % PEG 4,000	Resolution 2.60 Å R-free 0.275
1BBR THE STRUCTURE OF RESIDUES 7-16 OF THE A ALPHA CHAIN OF HUMAN FIBRINOGEN BOUND TO BOVINE THROMBIN AT 2.3 ANGSTROMS RESOLUTION Deposited 1992-04-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 517–625（109 aa） Chain H 367–516（150 aa） Chain L 318–366（49 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1BBR THE STRUCTURE OF RESIDUES 7-16 OF THE A ALPHA CHAIN OF HUMAN FIBRINOGEN BOUND TO BOVINE THROMBIN AT 2.3 ANGSTROMS RESOLUTION Deposited 1992-04-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 318–366（49 aa） Chain K 367–625（259 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1BBR THE STRUCTURE OF RESIDUES 7-16 OF THE A ALPHA CHAIN OF HUMAN FIBRINOGEN BOUND TO BOVINE THROMBIN AT 2.3 ANGSTROMS RESOLUTION Deposited 1992-04-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain M 318–366（49 aa） Chain N 367–625（259 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1BBR THE STRUCTURE OF RESIDUES 7-16 OF THE A ALPHA CHAIN OF HUMAN FIBRINOGEN BOUND TO BOVINE THROMBIN AT 2.3 ANGSTROMS RESOLUTION Deposited 1992-04-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain J 318–366（49 aa） Chain K 367–625（259 aa） Chain M 318–366（49 aa） Chain N 367–625（259 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1ETR REFINED 2.3 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF BOVINE THROMBIN COMPLEXES FORMED WITH THE BENZAMIDINE AND ARGININE-BASED THROMBIN INHIBITORS NAPAP, 4-TAPAP AND MQPA: A STARTING POINT FOR IMPROVING ANTITHROMBOTICS Deposited 1992-07-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain H 367–625（259 aa） Chain L 318–366（49 aa）	Not recorded	MIT amino{[(4S)-5-[(2R,4R)-2-carboxy-4-methylpiperidin-1-yl]-4-({[(3R)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonyl}amino)-5-oxopentyl]amino}methaniminium × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1ETS REFINED 2.3 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF BOVINE THROMBIN COMPLEXES FORMED WITH THE BENZAMIDINE AND ARGININE-BASED THROMBIN INHIBITORS NAPAP, 4-TAPAP AND MQPA: A STARTING POINT FOR IMPROVING ANTITHROMBOTICS Deposited 1992-07-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain H 367–625（259 aa） Chain L 318–366（49 aa）	Not recorded	MID 1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl-D-phenylalanyl]piperidine × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1ETT REFINED 2.3 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF BOVINE THROMBIN COMPLEXES FORMED WITH THE BENZAMIDINE AND ARGININE-BASED THROMBIN INHIBITORS NAPAP, 4-TAPAP AND MQPA: A STARTING POINT FOR IMPROVING ANTITHROMBOTICS Deposited 1992-07-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain H 367–625（259 aa） Chain L 318–366（49 aa）	Not recorded	4QQ 4-[(2S)-2-{[(4-methylphenyl)sulfonyl]amino}-3-oxo-3-(piperidin-1-yl)propyl]benzene-1-carboximidamide × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1HRT THE STRUCTURE OF A COMPLEX OF BOVINE ALPHA-THROMBIN AND RECOMBINANT HIRUDIN AT 2.8 ANGSTROMS RESOLUTION Deposited 1993-02-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 367–625（259 aa） Chain L 318–366（49 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1ID5 CRYSTAL STRUCTURE OF BOVINE THROMBIN COMPLEX WITH PROTEASE INHIBITOR ECOTIN Deposited 2001-04-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain H 367–622（256 aa） Fragment：THROMBIN HEAVY CHAIN Chain L 318–366（49 aa） Fragment：THROMBIN LIGHT CHAIN	Not recorded	CA CALCIUM ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；PEG6K, Citric Acid, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.264
1MKW THE CO-CRYSTAL STRUCTURE OF UNLIGANDED BOVINE ALPHA-THROMBIN AND PRETHROMBIN-2: MOVEMENT OF THE YPPW SEGMENT AND ACTIVE SITE RESIDUES UPON LIGAND BINDING Deposited 1997-03-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain H 367–625（259 aa） Chain L 318–366（49 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；24% POLYETHYLENE GLYCOL 2000, 0.1M SODIUM ACETATE, PH 4.6, 0.2M AMMONIUM SULFATE	Resolution 2.30 Å R-free 0.282
1MKW THE CO-CRYSTAL STRUCTURE OF UNLIGANDED BOVINE ALPHA-THROMBIN AND PRETHROMBIN-2: MOVEMENT OF THE YPPW SEGMENT AND ACTIVE SITE RESIDUES UPON LIGAND BINDING Deposited 1997-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain K 318–625（308 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；24% POLYETHYLENE GLYCOL 2000, 0.1M SODIUM ACETATE, PH 4.6, 0.2M AMMONIUM SULFATE	Resolution 2.30 Å R-free 0.282
1MKX THE CO-CRYSTAL STRUCTURE OF UNLIGANDED BOVINE ALPHA-THROMBIN AND PRETHROMBIN-2: MOVEMENT OF THE YPPW SEGMENT AND ACTIVE SITE RESIDUES UPON LIGAND BINDING Deposited 1997-03-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain H 367–625（259 aa） Chain L 318–366（49 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；38% AMMONIUM SULFATE, 0.25M AMMONIUM PHOSPHATE, PH 5.8, 1% POLYETHYLENE GLYCOL 4000 (DROP ONLY).	Resolution 2.20 Å R-free 0.255
1MKX THE CO-CRYSTAL STRUCTURE OF UNLIGANDED BOVINE ALPHA-THROMBIN AND PRETHROMBIN-2: MOVEMENT OF THE YPPW SEGMENT AND ACTIVE SITE RESIDUES UPON LIGAND BINDING Deposited 1997-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain K 318–625（308 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；38% AMMONIUM SULFATE, 0.25M AMMONIUM PHOSPHATE, PH 5.8, 1% POLYETHYLENE GLYCOL 4000 (DROP ONLY).	Resolution 2.20 Å R-free 0.255
1MKX THE CO-CRYSTAL STRUCTURE OF UNLIGANDED BOVINE ALPHA-THROMBIN AND PRETHROMBIN-2: MOVEMENT OF THE YPPW SEGMENT AND ACTIVE SITE RESIDUES UPON LIGAND BINDING Deposited 1997-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain H 367–625（259 aa） Chain K 318–625（308 aa） Chain L 318–366（49 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；38% AMMONIUM SULFATE, 0.25M AMMONIUM PHOSPHATE, PH 5.8, 1% POLYETHYLENE GLYCOL 4000 (DROP ONLY).	Resolution 2.20 Å R-free 0.255
1MKX THE CO-CRYSTAL STRUCTURE OF UNLIGANDED BOVINE ALPHA-THROMBIN AND PRETHROMBIN-2: MOVEMENT OF THE YPPW SEGMENT AND ACTIVE SITE RESIDUES UPON LIGAND BINDING Deposited 1997-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain K 318–625（308 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；38% AMMONIUM SULFATE, 0.25M AMMONIUM PHOSPHATE, PH 5.8, 1% POLYETHYLENE GLYCOL 4000 (DROP ONLY).	Resolution 2.20 Å R-free 0.255
1MKX THE CO-CRYSTAL STRUCTURE OF UNLIGANDED BOVINE ALPHA-THROMBIN AND PRETHROMBIN-2: MOVEMENT OF THE YPPW SEGMENT AND ACTIVE SITE RESIDUES UPON LIGAND BINDING Deposited 1997-03-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain H 367–625（259 aa） Chain K 318–625（308 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；38% AMMONIUM SULFATE, 0.25M AMMONIUM PHOSPHATE, PH 5.8, 1% POLYETHYLENE GLYCOL 4000 (DROP ONLY).	Resolution 2.20 Å R-free 0.255
1MKX THE CO-CRYSTAL STRUCTURE OF UNLIGANDED BOVINE ALPHA-THROMBIN AND PRETHROMBIN-2: MOVEMENT OF THE YPPW SEGMENT AND ACTIVE SITE RESIDUES UPON LIGAND BINDING Deposited 1997-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain L 318–366（49 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；38% AMMONIUM SULFATE, 0.25M AMMONIUM PHOSPHATE, PH 5.8, 1% POLYETHYLENE GLYCOL 4000 (DROP ONLY).	Resolution 2.20 Å R-free 0.255
1NL1 BOVINE PROTHROMBIN FRAGMENT 1 IN COMPLEX WITH CALCIUM ION Deposited 2003-01-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 44–190（147 aa） Fragment：fragment 1 (residues 1-156)	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；pH 7.6	Resolution 1.90 Å R-free 0.253
1NL2 BOVINE PROTHROMBIN FRAGMENT 1 IN COMPLEX WITH CALCIUM AND LYSOPHOSPHOTIDYLSERINE Deposited 2003-01-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 44–189（146 aa） Fragment：FRAGMENT 1 (residues 1-156)	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 7 CL CHLORIDE ION × 3 LPS O-{HYDROXY[((2R)-2-HYDROXY-3-{[(1S)-1-HYDROXYPENTADECYL]OXY}PROPYL)OXY]PHOSPHORYL}-L-SERINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；pH 7.6	Resolution 2.30 Å R-free 0.274
1TBQ CRYSTAL STRUCTURE OF INSECT DERIVED DOUBLE DOMAIN KAZAL INHIBITOR RHODNIIN IN COMPLEX WITH THROMBIN Deposited 1995-03-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 367–625（259 aa） Chain L 318–366（49 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.10 Å
1TBQ CRYSTAL STRUCTURE OF INSECT DERIVED DOUBLE DOMAIN KAZAL INHIBITOR RHODNIIN IN COMPLEX WITH THROMBIN Deposited 1995-03-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 318–366（49 aa） Chain K 367–625（259 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.10 Å
1TBR CRYSTAL STRUCTURE OF INSECT DERIVED DOUBLE DOMAIN KAZAL INHIBITOR RHODNIIN IN COMPLEX WITH THROMBIN Deposited 1995-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain H 367–625（259 aa） Chain J 318–366（49 aa） Chain K 367–625（259 aa） Chain L 318–366（49 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.263
1TBR CRYSTAL STRUCTURE OF INSECT DERIVED DOUBLE DOMAIN KAZAL INHIBITOR RHODNIIN IN COMPLEX WITH THROMBIN Deposited 1995-03-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 367–625（259 aa） Chain L 318–366（49 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.263
1TBR CRYSTAL STRUCTURE OF INSECT DERIVED DOUBLE DOMAIN KAZAL INHIBITOR RHODNIIN IN COMPLEX WITH THROMBIN Deposited 1995-03-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 318–366（49 aa） Chain K 367–625（259 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.263
1TOC STRUCTURE OF SERINE PROTEINASE Deposited 1996-07-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 318–366（49 aa） Chain B 367–625（259 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.10 Å
1TOC STRUCTURE OF SERINE PROTEINASE Deposited 1996-07-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 318–366（49 aa） Chain D 367–625（259 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.10 Å
1TOC STRUCTURE OF SERINE PROTEINASE Deposited 1996-07-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 318–366（49 aa） Chain H 367–625（259 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.10 Å
1TOC STRUCTURE OF SERINE PROTEINASE Deposited 1996-07-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 318–366（49 aa） Chain F 367–625（259 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.10 Å
1UCY THROMBIN COMPLEXED WITH FIBRINOPEPTIDE A ALPHA (RESIDUES 7-19). THREE COMPLEXES, ONE WITH EPSILON-THROMBIN AND TWO WITH ALPHA-THROMBIN Deposited 1996-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 517–625（109 aa） Chain H 367–516（150 aa） Chain L 318–366（49 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1UCY THROMBIN COMPLEXED WITH FIBRINOPEPTIDE A ALPHA (RESIDUES 7-19). THREE COMPLEXES, ONE WITH EPSILON-THROMBIN AND TWO WITH ALPHA-THROMBIN Deposited 1996-08-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 318–366（49 aa） Chain K 367–625（259 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1UCY THROMBIN COMPLEXED WITH FIBRINOPEPTIDE A ALPHA (RESIDUES 7-19). THREE COMPLEXES, ONE WITH EPSILON-THROMBIN AND TWO WITH ALPHA-THROMBIN Deposited 1996-08-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain M 318–366（49 aa） Chain N 367–625（259 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1UVT BOVINE THROMBIN--BM14.1248 COMPLEX Deposited 1996-10-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain H 367–625（259 aa） Chain L 318–366（49 aa）	Not recorded	I48 N-{3-METHYL-5-[2-(PYRIDIN-4-YLAMINO)-ETHOXY]-PHENYL}-BENZENESULFONAMIDE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1UVU BOVINE THROMBIN--BM12.1700 COMPLEX Deposited 1996-10-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain H 367–625（259 aa） Chain L 318–366（49 aa）	Not recorded	DCH 3-(7-DIAMINOMETHYL-NAPHTHALEN-2-YL)-PROPIONIC ACID ETHYL ESTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1VIT THROMBIN:HIRUDIN 51-65 COMPLEX Deposited 1996-01-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 367–625（259 aa） Chain L 318–366（49 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；HANGING DROP, RESERVOIRS CONTAINING 39% SATURATED AMMONIUM SULFATE, 0.25 M AMMONIUM PHOSPHATE PH 8.0 AND 1% PEG4000. DROPS CONSISTED OF EQUAL VOLUMES OF RESERVOIR AND PROTEIN SOLUTION CONTAINING 23.5 MG/ML PROTEIN., vapor diffusion - hanging drop	Resolution 3.20 Å
1VIT THROMBIN:HIRUDIN 51-65 COMPLEX Deposited 1996-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 367–516（150 aa） Chain G 517–625（109 aa） Chain M 318–366（49 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；HANGING DROP, RESERVOIRS CONTAINING 39% SATURATED AMMONIUM SULFATE, 0.25 M AMMONIUM PHOSPHATE PH 8.0 AND 1% PEG4000. DROPS CONSISTED OF EQUAL VOLUMES OF RESERVOIR AND PROTEIN SOLUTION CONTAINING 23.5 MG/ML PROTEIN., vapor diffusion - hanging drop	Resolution 3.20 Å
1YCP THE CRYSTAL STRUCTURE OF FIBRINOGEN-AA PEPTIDE 1-23 (F8Y) BOUND TO BOVINE THROMBIN EXPLAINS WHY THE MUTATION OF PHE-8 TO TYROSINE STRONGLY INHIBITS NORMAL CLEAVAGE AT ARGININE-16 Deposited 1997-05-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 367–625（259 aa） Chain L 318–366（49 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；2.0M AMMONIUM SULFATE 0.1M HEPES, PH 7.5 2.0% POLYETHYLENE GLYCOL 400	Resolution 2.50 Å R-free 0.245
1YCP THE CRYSTAL STRUCTURE OF FIBRINOGEN-AA PEPTIDE 1-23 (F8Y) BOUND TO BOVINE THROMBIN EXPLAINS WHY THE MUTATION OF PHE-8 TO TYROSINE STRONGLY INHIBITS NORMAL CLEAVAGE AT ARGININE-16 Deposited 1997-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain J 318–366（49 aa） Chain K 367–516（150 aa） Chain M 517–625（109 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；2.0M AMMONIUM SULFATE 0.1M HEPES, PH 7.5 2.0% POLYETHYLENE GLYCOL 400	Resolution 2.50 Å R-free 0.245
2A1D Staphylocoagulase bound to bovine thrombin Deposited 2005-06-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 326–366（41 aa） Fragment：Thrombin light chain Chain B 367–625（259 aa） Fragment：Thrombin heavy chain	Not recorded	0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1M IMIDAZOLE, 0.2M AMMONIUM FORMATE, 12% POLYETHYLENE GLYCOL 4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.50 Å R-free 0.306
2A1D Staphylocoagulase bound to bovine thrombin Deposited 2005-06-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 326–366（41 aa） Fragment：Thrombin light chain Chain F 367–625（259 aa） Fragment：Thrombin heavy chain	Not recorded	0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1M IMIDAZOLE, 0.2M AMMONIUM FORMATE, 12% POLYETHYLENE GLYCOL 4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.50 Å R-free 0.306
2HPP Structures of the noncovalent complexes of human and bovine prothrombin fragment 2 with human ppack-thrombin Deposited 1993-04-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 214–292（79 aa） Fragment：UNP residues 214-292	Not recorded	0G7 D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-prolinamide × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.30 Å
2ODY Thrombin-bound boophilin displays a functional and accessible reactive-site loop Deposited 2006-12-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 318–366（49 aa） Fragment：Thrombin light chain, residues 318-366 Chain B 367–625（259 aa） Fragment：Thrombin heavy chain, residues 367-625	Not recorded	PO4 PHOSPHATE ION × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；279 K；18% PEG 8000, 0.05M Potassium phosphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 279K	Resolution 2.35 Å R-free 0.230
2ODY Thrombin-bound boophilin displays a functional and accessible reactive-site loop Deposited 2006-12-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 318–366（49 aa） Fragment：Thrombin light chain, residues 318-366 Chain D 367–625（259 aa） Fragment：Thrombin heavy chain, residues 367-625	Not recorded	PO4 PHOSPHATE ION × 1 NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；279 K；18% PEG 8000, 0.05M Potassium phosphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 279K	Resolution 2.35 Å R-free 0.230
2PF1 STRUCTURE OF BOVINE PROTHROMBIN FRAGMENT 1 REFINED AT 2.25 ANGSTROMS RESOLUTION Deposited 1992-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 44–199（156 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
2PF2 THE CA+2 ION AND MEMBRANE BINDING STRUCTURE OF THE GLA DOMAIN OF CA-PROTHROMBIN FRAGMENT 1 Deposited 1991-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 44–199（156 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 7	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
2SPT DIFFERENCES IN THE METAL ION STRUCTURE BETWEEN SR-AND CA-PROTHROMBIN FRAGMENT 1 Deposited 1994-02-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 44–188（145 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SR STRONTIUM ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
3PMA 2.2 Angstrom crystal structure of the complex between Bovine Thrombin and Sucrose Octasulfate Deposited 2010-11-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 336–364（29 aa） Fragment：Bovine Thrombin Light Chain residues 336-364 Chain B 367–625（259 aa）	Not recorded	NA SODIUM ION × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；295 K；3 microliters Bovine thrombin, 7 mg/ml in 0.01M Tris-HCl, ph 8.0, 0.05M NaCl, 0.1M sodium citrate, 20% w/v, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.245
3PMA 2.2 Angstrom crystal structure of the complex between Bovine Thrombin and Sucrose Octasulfate Deposited 2010-11-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 336–364（29 aa） Fragment：Bovine Thrombin Light Chain residues 336-364 Chain D 367–625（259 aa）	Not recorded	NA SODIUM ION × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；295 K；3 microliters Bovine thrombin, 7 mg/ml in 0.01M Tris-HCl, ph 8.0, 0.05M NaCl, 0.1M sodium citrate, 20% w/v, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.245
3PMA 2.2 Angstrom crystal structure of the complex between Bovine Thrombin and Sucrose Octasulfate Deposited 2010-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 336–364（29 aa） Fragment：Bovine Thrombin Light Chain residues 336-364 Chain B 367–625（259 aa） Chain C 336–364（29 aa） Fragment：Bovine Thrombin Light Chain residues 336-364 Chain D 367–625（259 aa）	Not recorded	NA SODIUM ION × 4 CIT CITRIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；295 K；3 microliters Bovine thrombin, 7 mg/ml in 0.01M Tris-HCl, ph 8.0, 0.05M NaCl, 0.1M sodium citrate, 20% w/v, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.245
3PMA 2.2 Angstrom crystal structure of the complex between Bovine Thrombin and Sucrose Octasulfate Deposited 2010-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 336–364（29 aa） Fragment：Bovine Thrombin Light Chain residues 336-364 Chain B 367–625（259 aa） Chain C 336–364（29 aa） Fragment：Bovine Thrombin Light Chain residues 336-364 Chain D 367–625（259 aa）	Not recorded	NA SODIUM ION × 2 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；295 K；3 microliters Bovine thrombin, 7 mg/ml in 0.01M Tris-HCl, ph 8.0, 0.05M NaCl, 0.1M sodium citrate, 20% w/v, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.245
3PMB 2.9 Angstrom crystal structure of bovine thrombin in tetragonal spacegroup Deposited 2010-11-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 336–364（29 aa） Fragment：Bovine Thrombin Light Chain residues 336-364 Chain B 367–625（259 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；295 K；3 microliters Bovine thrombin, 7 mg/ml in 0.01M Tris-HCl, ph 8.0, 0.05M NaCl, 0.1M sodium citrate, 20% w/v PEG3350, 15% v/v 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.90 Å R-free 0.301
3PMB 2.9 Angstrom crystal structure of bovine thrombin in tetragonal spacegroup Deposited 2010-11-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 336–364（29 aa） Fragment：Bovine Thrombin Light Chain residues 336-364 Chain D 367–625（259 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；295 K；3 microliters Bovine thrombin, 7 mg/ml in 0.01M Tris-HCl, ph 8.0, 0.05M NaCl, 0.1M sodium citrate, 20% w/v PEG3350, 15% v/v 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.90 Å R-free 0.301
7A0D The Crystal Structure of Bovine Thrombin in complex with Hirudin (C16U/C28U) at 1.6 Angstroms Resolution Deposited 2020-08-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain HHH 367–625（259 aa） Chain LLL 318–366（49 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；297 K；38% PEG 4000, 0.1 M sodium phosphate (pH= 4.7), 0.2 M NaCl	Resolution 1.60 Å R-free 0.215
7A0E The Crystal Structure of Bovine Thrombin in complex with Hirudin (C6U/C14U) at 1.9 Angstroms Resolution Deposited 2020-08-07	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain HHH 367–625（259 aa） Chain LLL 318–366（49 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；297 K；38% PEG 4000, 0.1 M sodium phosphate (pH= 4.7), and 0.2 M NaCl	Resolution 1.90 Å R-free 0.263

30 other PDB entries and 55 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	THRB_BOVIN
Isoform	—
PDB entities	1, 3
Chains and sequence ranges	Author chain HHH； PDBConstruct 1–259； UniProt 367–625 Author chain LLL； PDBConstruct 1–49； UniProt 318–366

Hirudin variant-1

OrganismNot specified

UniProt P01050

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain III； UniProt 1–65	Mutation：C22U/C39U	Prothrombin × 1 （P00735） Prothrombin × 1 （P00735） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.7；297 K；38% PEG 4000, 0.1 M sodium phosphate (pH= 4.7), 0.3 M NaCl	Resolution 2.70 Å R-free 0.253

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7A0F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AD8 COMPLEX OF THROMBIN WITH AND INHIBITOR CONTAINING A NOVEL P1 MOIETY Deposited 1997-02-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 55–64（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 1 MDL [DEHYDROXY-N-METHYL-TYROSYL-PROLINYL]-[4,4,5,5,5-PENTAFLUORO-3-OXY-1-[3-INDOLYL]-PENT-2-YL]AMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；A DROP WITH 1.62 MG/ML PROTEIN, 0.375 M NACL, 0.09 M PHOSPHATE BUFFER (PH 7.3), 0.5 MM AZIDE, 4.9 MM INHIBITOR AND 15% (W/V) PEG8000 WAS EQUILIBRATED AGAINST 30% (W/V)PEG8000 IN 0.08 M PHOSPHATE BUFFER (PH 7.3), USING A HANGING DROP SETUP., vapor diffusion - hanging drop	Resolution 2.00 Å
1AY6 THROMBIN INHIBITOR FROM THEONALLA, CYCLOTHEANAMIDE-BASED MACROCYCLIC TRIPEPTIDE MOTIF Deposited 1997-11-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 55–64（10 aa） Fragment：residues 55-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	1ZV amino({3-[(3R,5R,14S,16S,21aR)-5,14-dihydroxy-1,4,17-trioxo-16-(2-phenylethyl)icosahydro-1H-pyrrolo[1,2-d][1,4,7,11]tetraazacyclononadecin-3-yl]propyl}amino)methaniminium × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；CRYSTALLIZED FROM 25% PEG 8K, 0.1M SOD. PHOSPHATE BUFFER PH 7.5. MACROSEEDED TO MAKE LARGER CRYSTALS	Resolution 1.80 Å
1BCU ALPHA-THROMBIN COMPLEXED WITH HIRUGEN AND PROFLAVIN Deposited 1998-05-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–65（12 aa） Fragment：RESIDUES 54-65 OF HIRUDIN	Non-standard monomer：Yes (specific site not provided by mmCIF)	PRL PROFLAVIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7	Resolution 2.00 Å R-free 0.212
1H8D X-ray structure of the human alpha-thrombin complex with a tripeptide phosphonate inhibitor. Deposited 2001-02-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 55–64（10 aa） Fragment：RESIDUES 55 TO 64	Non-standard monomer：Yes (specific site not provided by mmCIF)	PHW N-[(benzyloxy)carbonyl]-beta-phenyl-D-phenylalanyl-N-{(1S,3E)-1-[dihydroxy(diphenoxy)-lambda~5~-phosphanyl]-4-methoxybut-3-en-1-yl}-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；20% PEG 8K, 0.05MM NAHPO4, 0.1M NACL, PH 7.20	Resolution 1.40 Å R-free 0.220
1H8I X-ray crystal structure of human alpha-thrombin with a tripeptide phosphonate inhibitor. Deposited 2001-02-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 55–64（10 aa） Fragment：RESIDUES 55 TO 64	Non-standard monomer：Yes (specific site not provided by mmCIF)	PHV N-[(benzyloxy)carbonyl]-beta-phenyl-D-phenylalanyl-N-[(1S)-4-methoxy-1-phosphonobutyl]-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；PH 7.20	Resolution 1.75 Å R-free 0.235
1HIC THE NMR SOLUTION STRUCTURE OF HIRUDIN(1-51) AND COMPARISON WITH CORRESPONDING THREE-DIMENSIONAL STRUCTURES DETERMINED USING THE COMPLETE 65-RESIDUE HIRUDIN POLYPEPTIDE CHAIN Deposited 1992-04-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–51（51 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1HRT THE STRUCTURE OF A COMPLEX OF BOVINE ALPHA-THROMBIN AND RECOMBINANT HIRUDIN AT 2.8 ANGSTROMS RESOLUTION Deposited 1993-02-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 1–65（65 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1HXE SERINE PROTEASE Deposited 1995-12-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 55–64（10 aa）	Not recorded	RB RUBIDIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1HXF HUMAN THROMBIN COMPLEX WITH HIRUDIN VARIANT Deposited 1996-09-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 55–64（10 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
2HIR SOLUTION STRUCTURE OF RECOMBINANT HIRUDIN AND THE LYS-47 (RIGHT ARROW) GLU MUTANT. A NUCLEAR MAGNETIC RESONANCE AND HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING STUDY Deposited 1988-12-19	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2JOO The NMR Solution Structure of Recombinant RGD-hirudin Deposited 2007-03-14	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Pressure ambient NMR sample composition 5 mM RGD-hirudin, 0.02mol/L Na2HPO4/NaH2PO4 buffer, pH 7.0, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2PW8 Crystal structure of sulfo-hirudin complexed to thrombin Deposited 2007-05-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 3–65（63 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NI NICKEL (II) ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.1M Tris, 20% PEG2K, 0.01M Nickel Chloride. , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.84 Å R-free 0.233
2V3O Thrombin with 3-cycle with F Deposited 2007-06-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 56–65（10 aa） Fragment：C-TERMINUS, RESIDUES 56-65	Non-standard monomer：Yes (specific site not provided by mmCIF)	I26 (2R)-[(4-CARBAMIMIDOYLPHENYL)AMINO]{3-[3-(DIMETHYLAMINO)-2,2-DIMETHYLPROPOXY]-5-ETHYL-2-FLUOROPHENYL}ETHANOIC ACID × 1 NA SODIUM ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.79 Å R-free 0.212
2ZC9 Thrombin in complex with Inhibitor Deposited 2007-11-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：UNP Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 2 22U D-phenylalanyl-N-(3-chlorobenzyl)-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.58 Å R-free 0.233
2ZDA Exploring Thrombin S1 pocket Deposited 2007-11-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：UNP Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 32U D-phenylalanyl-N-{4-[amino(iminio)methyl]benzyl}-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.73 Å R-free 0.228
2ZDV Exploring Thrombin S1 pocket Deposited 2007-11-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：UNP Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 37U D-phenylalanyl-N-(3-fluorobenzyl)-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.72 Å R-free 0.243
2ZF0 Exploring Thrombin S1 Pocket Deposited 2007-12-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：UNP Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 2 51U D-phenylalanyl-N-(3-methylbenzyl)-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.267
2ZFF Exploring Thrombin S1-pocket Deposited 2008-01-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：UNP Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 2 53U D-phenylalanyl-N-benzyl-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.47 Å R-free 0.203
2ZFP Thrombin Inibition Deposited 2008-01-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：UNP Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 2 19U 1-[(2R)-2-aminobutanoyl]-N-(3-chlorobenzyl)-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.25 Å R-free 0.298
2ZGB Thrombin Inhibition Deposited 2008-01-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：UNP Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 2 21U D-leucyl-N-(3-chlorobenzyl)-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.60 Å R-free 0.231
2ZGX Thrombin Inhibition Deposited 2008-01-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：UNP Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 2 29U 1-[(2R)-2-aminobutanoyl]-N-(4-carbamimidoylbenzyl)-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.229
2ZHQ Thrombin Inhibition Deposited 2008-02-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：UNP Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 2 27U N-(4-carbamimidoylbenzyl)-1-(3-phenylpropanoyl)-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.96 Å R-free 0.272
2ZI2 Thrombin Inhibition Deposited 2008-02-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：UNP Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 2 24U 1-butanoyl-N-(4-carbamimidoylbenzyl)-L-prolinamide × 1 BEN BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.65 Å R-free 0.225
2ZIQ Thrombin Inhibition Deposited 2008-02-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	26U N-(4-carbamimidoylbenzyl)-1-(4-methylpentanoyl)-L-prolinamide × 1 NA SODIUM ION × 2 BEN BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.65 Å R-free 0.225
2ZNK Thrombin Inhibition Deposited 2008-04-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	31U D-leucyl-N-(4-carbamimidoylbenzyl)-L-prolinamide × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.229
2ZO3 Bisphenylic Thrombin Inhibitors Deposited 2008-05-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	33U beta-phenyl-D-phenylalanyl-N-(4-carbamimidoylbenzyl)-L-prolinamide × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.250
3D49 Thrombin Inhibition Deposited 2008-05-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：UNP Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 2 BEN BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate Buffer, Sodium Chloride, PEG 8000 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.50 Å R-free 0.237
3DHK Bisphenylic Thrombin Inhibitors Deposited 2008-06-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	23U beta-phenyl-D-phenylalanyl-N-(3-chlorobenzyl)-L-prolinamide × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.73 Å R-free 0.249
3DT0 Understanding Thrombin Inhibition Deposited 2008-07-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	16U N-(3-chlorobenzyl)-1-(4-methylpentanoyl)-L-prolinamide × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.40 Å R-free 0.286
3DUX Understanding Thrombin Inhibition Deposited 2008-07-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	64U 3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.60 Å R-free 0.247
3EGK KNOBLE Inhibitor Deposited 2008-09-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	M18 {(2S)-1-[N-(tert-butoxycarbonyl)glycyl]pyrrolidin-2-yl}methyl (3-chlorophenyl)acetate × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.312
3EQ0 Thrombin Inhibitor Deposited 2008-09-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：Residues 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	2TS (2S)-N-[[2-(aminomethyl)-5-chloro-phenyl]methyl]-1-[(2R)-5-carbamimidamido-2-(phenylmethylsulfonylamino)pentanoyl]pyrrolidine-2-carboxamide × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.53 Å R-free 0.249
3LDX Discovery and Clinical Evaluation of RWJ-671818, a Thrombin Inhibitor with an Oxyguanidine P1 Motif Deposited 2010-01-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 55–65（11 aa） Fragment：residues 55-65	Not recorded	NLI N-[2-(carbamimidamidooxy)ethyl]-2-{3-[(2,2-difluoro-2-phenylethyl)amino]-6-methyl-2-oxopyrazin-1(2H)-yl}acetamide × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.25 Å R-free 0.224
3UTU High affinity inhibitor of human thrombin Deposited 2011-11-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 54–64（11 aa） Fragment：UNP RESIDUES 54-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	1TS (2S)-N-[(4-carbamimidoylphenyl)methyl]-1-[(2S)-2-[(3-chloro-4-methoxybenzene)sulfonamido]-3-{[(4-cyanophenyl)methyl]carbamoyl}propanoyl]pyrrolidine-2-carboxamide × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PHOSPHATE BUFFER, SODIUM CHLORIDE, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.55 Å R-free 0.271
4AX9 Human thrombin complexed with Napsagatran, RO0466240 Deposited 2012-06-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 55–65（11 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 55-65	Not recorded	NA SODIUM ION × 2 N5N 2-[[(2S)-4-[[(3S)-1-carbamimidoylpiperidin-3-yl]methylamino]-2-(naphthalen-2-ylsulfonylamino)-4-oxidanylidene-butanoyl] -cyclopropyl-amino]ethanoic acid × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.196
4BAH Thrombin in complex with inhibitor Deposited 2012-09-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 53–64（12 aa） Fragment：RESIDUES 62-71	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MEL [((1R)-2-{(2S)-2-[({4-[AMINO(IMINO)METHYL]BENZYL}AMINO)CARBONYL]AZETIDINYL}-1-CYCLOHEXYL-2-OXOETHYL)AMINO]ACETIC ACID × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.94 Å R-free 0.194
4BAK Thrombin in complex with inhibitor Deposited 2012-09-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 53–64（12 aa） Fragment：RESIDUES 62-71	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 M67 (2S)-N-(4-CARBAMIMIDOYLBENZYL)-1-[(2R)-2-CYCLOHEXYL-2-{[2-OXO-2-(PROPYLAMINO)ETHYL]AMINO}ACETYL]AZETIDINE-2-CARBOXAMIDE × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.94 Å R-free 0.203
4BAM Thrombin in complex with inhibitor Deposited 2012-09-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 53–64（12 aa） Fragment：RESIDUES 53-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MM9 (2S)-N-[(4-carbamimidoylphenyl)methyl]-1-[(2R)-2-cyclohexyl-2-[[2-(dimethylamino)-2-oxidanylidene-ethyl]amino]ethanoyl]azetidine-2-carboxamide × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.88 Å R-free 0.195
4BAN Thrombin in complex with inhibitor Deposited 2012-09-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 53–64（12 aa） Fragment：RESIDUES 53-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 M6S (2S)-N-[(4-carbamimidoylphenyl)methyl]-1-[(2R)-2-cyclohexyl-2-[[2-(methylamino)-2-oxidanylidene-ethyl]amino]ethanoyl]azetidine-2-carboxamide × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.87 Å R-free 0.203
4BAQ Thrombin in complex with inhibitor Deposited 2012-09-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 53–64（12 aa） Fragment：RESIDUES 53-64	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 M4Z (2S)-N-[(4-carbamimidoylphenyl)methyl]-1-[(2R)-2-cyclohexyl-2-[[2-(ethylamino)-2-oxidanylidene-ethyl]amino]ethanoyl]azetidine-2-carboxamide × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.89 Å R-free 0.221
4HIR SOLUTION STRUCTURE OF RECOMBINANT HIRUDIN AND THE LYS-47 (RIGHT ARROW) GLU MUTANT. A NUCLEAR MAGNETIC RESONANCE AND HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING STUDY Deposited 1988-12-19	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
4LXB Crystal Structure Analysis of thrombin in complex with compound D58 Deposited 2013-07-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 53–65（13 aa） Fragment：unp residues 53-65	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 7R9 5-Chloro-thiophene-2-carboxylic acid [(S)-2-[2-difluoromethoxy-3-(2-oxo-piperidin-1-yl)-benzenesulfonylamino]-3-((S)-3-dimethylamino-pyrrolidin-1-yl)-3-oxo-propyl]-amide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；0.1 M SODIUM PHASPHATE PH=7.3, 20% PEG8000, 5MG/ML THROMBIN, 0.2 M NACL, 1 mM INHIBNITOR, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.61 Å R-free 0.228
4MLF Crystal structure for the complex of thrombin mutant D102N and hirudin Deposited 2013-09-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–65（65 aa）	Not recorded	NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；20% PEG 3350, 0.2M Ca acetate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.234
4YES Thrombin in complex with (S)-(4-chloro-2-((1-(5-methyl-1H-pyrrole-2-carbonyl)pyrrolidine-2-carboxamido)methyl)phenyl)methanaminium Deposited 2015-02-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 54–65（12 aa） Fragment：UNP residues 54-65	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1 GOL GLYCEROL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 45S N-[2-(aminomethyl)-5-chlorobenzyl]-1-[(5-methyl-1H-pyrrol-2-yl)carbonyl]-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；28 % PEG 2000 MMe, 100mM BisTris	Resolution 1.50 Å R-free 0.234
5HIR SOLUTION STRUCTURE OF RECOMBINANT HIRUDIN AND THE LYS-47 (RIGHT ARROW) GLU MUTANT. A NUCLEAR MAGNETIC RESONANCE AND HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING STUDY Deposited 1990-01-09	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
6HIR SOLUTION STRUCTURE OF RECOMBINANT HIRUDIN AND THE LYS-47 (RIGHT ARROW) GLU MUTANT. A NUCLEAR MAGNETIC RESONANCE AND HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING STUDY Deposited 1990-01-09	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–65（65 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
7A0D The Crystal Structure of Bovine Thrombin in complex with Hirudin (C16U/C28U) at 1.6 Angstroms Resolution Deposited 2020-08-07	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain III 1–65（65 aa）	Mutation：C16U/C28U	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；297 K；38% PEG 4000, 0.1 M sodium phosphate (pH= 4.7), 0.2 M NaCl	Resolution 1.60 Å R-free 0.215
7A0E The Crystal Structure of Bovine Thrombin in complex with Hirudin (C6U/C14U) at 1.9 Angstroms Resolution Deposited 2020-08-07	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain III 1–65（65 aa）	Mutation：C6U/C14U	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；297 K；38% PEG 4000, 0.1 M sodium phosphate (pH= 4.7), and 0.2 M NaCl	Resolution 1.90 Å R-free 0.263

48 other PDB entries and 48 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HIRV1_HIRME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain III； PDBConstruct 1–65； UniProt 1–65

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7a0f
Deposition date deposition_date	2020-08-07
Structure title title	The Crystal Structure of Bovine Thrombin in complex with Hirudin (C22U/C39U) at 2.7 Angstroms Resolution
Keywords keywords	Hydrolase, Inhibitor, Hirudin, Thrombin, Selenocysteine, Derivative; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.93 Å
Radius of gyration Rg (electron density) rg_electron	19.72 Å
Forward intensity I(0) i0	29264100.00
Molecular weight molecular_weight	40852.0 kDa
Excluded volume excluded_volume	50779 Å³
Envelope volume envelope_volume	58941 Å³
Hydration-shell volume shell_volume	24115 Å³
Envelope diameter envelope_diameter	69.6 Å
Shell Rg shell_rg	27.19 Å
Envelope Rg envelope_rg	20.18 Å
Shape Rg shape_rg	19.69 Å
Total Rg total_rg	20.76 Å
Total atoms total_atoms	2863
Residues n_residues	359
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	68.0 Å
Rg (real space) rg_real	20.81 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	2.9260e+07
I(0) uncertainty (real space) i0_real_error	3.8980e+05
Rg (reciprocal space) rg_reciprocal	20.83 Å
I(0) (reciprocal space) i0_reciprocal	29260000.0000
Solution quality estimate total_estimate	0.8842
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.6 Å
Skewness Skewness skewness	0.202
Kurtosis Kurtosis kurtosis	-0.319
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7010000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Prothrombin
Molecular weight formula_weight	29772.4 kDa
EC 编号 ec_number	3.4.21.5
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	HHH
Atom count atom_count	2936

IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLLVRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCLPDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIRITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDRLGS

Entity 2 Entity 2 polymer

Description description	Hirudin variant-1
Molecular weight formula_weight	7067.3 kDa
Mutation mutation	C22U/C39U
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	III

VVYTDCTESGQNLCLCEGSNVUGQGNKCILGSDGEKNQUVTGEGTPKPQSHNDGDFEEIPEEYLQ

Entity 3 Entity 3 polymer

Description description	Prothrombin
Molecular weight formula_weight	5735.2 kDa
EC 编号 ec_number	3.4.21.5
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	LLL

TSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGR

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	73

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8. Citations (1)

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Unit-cell length a length_a	58.069 Å
Unit-cell length b length_b	101.498 Å
Unit-cell length c length_c	142.075 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	47.790 Å
R factor r_factor	—
R_work r_work	0.1936
R_free r_free	0.2532

fit	/app/data/saxs_computation/a0/7a0f/7a0f.fit
pddf	/app/data/pr_computation/a0/7a0f/7a0f.pr.out
profile	/app/data/saxs_computation/a0/7a0f/7a0f.dat

The Crystal Structure of Bovine Thrombin in complex with Hirudin (C22U/C39U) at 2.7 Angstroms Resolution

1. Protein Identity and Related Structures Protein Identity & Related Structures

Prothrombin

State in the Current Structure

Other States of the Same Protein in the Database

Hirudin variant-1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)