2ody

Thrombin-bound boophilin displays a functional and accessible reactive-site loop

Method: X-RAY DIFFRACTION D_max: 98.0 Å Quality: EXCELLENT

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

Prothrombin (EC 3.4.21.5)

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 A； UniProt 318–366 Chain B； UniProt 367–625	Fragment：Thrombin light chain, residues 318-366 Fragment：Thrombin heavy chain, residues 367-625	Boophilin × 1 （Q8WPI2） 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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 318–366 Chain D； UniProt 367–625	Fragment：Thrombin light chain, residues 318-366 Fragment：Thrombin heavy chain, residues 367-625	Boophilin × 1 （Q8WPI2） 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

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 2ODY	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 construct 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 construct 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 construct 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 construct 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 construct 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 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） 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 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） 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 construct 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 construct 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 construct 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 construct 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 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 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 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 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 construct 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 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 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
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 construct 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 construct Different ligand/ion 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
7A0F The Crystal Structure of Bovine Thrombin in complex with Hirudin (C22U/C39U) at 2.7 Angstroms Resolution Deposited 2020-08-07	Different construct Different ligand/ion 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), 0.3 M NaCl	Resolution 2.70 Å R-free 0.253

30 other PDB entries and 54 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	THRB_BOVIN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 22–49； UniProt 318–366 Author chain C； PDBConstruct 22–48； UniProt 318–366 Author chain B； PDBConstruct 1–259； UniProt 367–625 Author chain D； PDBConstruct 1–259； UniProt 367–625

Boophilin

Rhipicephalus microplus

UniProt Q8WPI2

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 E； UniProt 16–142	Fragment：Boophilin (isoform H2), Residues 16-142	Prothrombin (EC 3.4.21.5) × 1 （P00735） Prothrombin (EC 3.4.21.5) × 1 （P00735） 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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 16–142	Fragment：Boophilin (isoform H2), Residues 16-142	Prothrombin (EC 3.4.21.5) × 1 （P00735） Prothrombin (EC 3.4.21.5) × 1 （P00735） 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

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q8WPI2_BOOMI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–127； UniProt 16–142 Author chain F； PDBConstruct 1–127； UniProt 16–142

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	2ody
Deposition date deposition_date	2006-12-27
Structure title title	Thrombin-bound boophilin displays a functional and accessible reactive-site loop
Keywords keywords	kunitz-type thrombin inhibitor, BLOOD CLOTTING-BLOOD CLOTTING INHIBITOR COMPLEX; BLOOD CLOTTING/BLOOD CLOTTING INHIBITOR
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	30.85 Å
Radius of gyration Rg (electron density) rg_electron	30.25 Å
Forward intensity I(0) i0	158840000.00
Molecular weight molecular_weight	97024.0 kDa
Excluded volume excluded_volume	120030 Å³
Envelope volume envelope_volume	150510 Å³
Hydration-shell volume shell_volume	40959 Å³
Envelope diameter envelope_diameter	108.8 Å
Shell Rg shell_rg	37.60 Å
Envelope Rg envelope_rg	30.35 Å
Shape Rg shape_rg	30.22 Å
Total Rg total_rg	30.96 Å
Total atoms total_atoms	6805
Residues n_residues	737
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	98.0 Å
Rg (real space) rg_real	30.78 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	1.5880e+08
I(0) uncertainty (real space) i0_real_error	2.3690e+06
Rg (reciprocal space) rg_reciprocal	30.81 Å
I(0) (reciprocal space) i0_reciprocal	158800000.0000
Solution quality estimate total_estimate	0.9010
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.6 Å
Skewness Skewness skewness	0.261
Kurtosis Kurtosis kurtosis	-0.479
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	28400000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.918

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Prothrombin (EC 3.4.21.5)
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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	7258

TSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGR

Entity 2 Entity 2 polymer

Description description	Prothrombin (EC 3.4.21.5)
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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLLVRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCLPDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIRITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDRLGS

Entity 3 Entity 3 polymer

Description description	Boophilin
Molecular weight formula_weight	14002.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

QRNGFCRLPADEGICKALIPRFYFNTETGKCTMFSYGGCGGNENNFETIEECQKACGAPERVNDFESADFKTGCEPAADSGSCAGQLERWFYNVQSGECETFVYGGCGGNDNNYESEEECELVCKNM

来源 Source

来源生物 organism	Rhipicephalus microplus
通用名 common_name	southern cattle tick
NCBI Class编号 ncbi_taxonomy_id	6941
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	4

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	2

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	453

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2odye1
Class class	g — Small proteins
Fold Fold fold	g.8 — BPTI-like
Superfamily Superfamily superfamily	g.8.1 — BPTI-like
Family Family family	g.8.1.0 — automated matches

Domain ID domain_id	d2odye2
Class class	g — Small proteins
Fold Fold fold	g.8 — BPTI-like
Superfamily Superfamily superfamily	g.8.1 — BPTI-like
Family Family family	g.8.1.0 — automated matches

Domain ID domain_id	d2odyf1
Class class	g — Small proteins
Fold Fold fold	g.8 — BPTI-like
Superfamily Superfamily superfamily	g.8.1 — BPTI-like
Family Family family	g.8.1.0 — automated matches

Domain ID domain_id	d2odyf2
Class class	g — Small proteins
Fold Fold fold	g.8 — BPTI-like
Superfamily Superfamily superfamily	g.8.1 — BPTI-like
Family Family family	g.8.1.0 — automated matches

CATH v4.4 (10 domains)

Domain ID domain_id	2odyA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	140 — Epsilon-Thrombin; Chain L
Homologous superfamily homologous superfamily	10 — Thrombin light chain domain

Domain ID domain_id	2odyB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	2odyB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	2odyC00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	140 — Epsilon-Thrombin; Chain L
Homologous superfamily homologous superfamily	10 — Thrombin light chain domain

Domain ID domain_id	2odyD01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	2odyD02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	2odyE01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

Domain ID domain_id	2odyE02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

Domain ID domain_id	2odyF01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

Domain ID domain_id	2odyF02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

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8. Citations (1)

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Unit-cell length a length_a	92.500 Å
Unit-cell length b length_b	104.200 Å
Unit-cell length c length_c	129.100 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	47.190 Å
R factor r_factor	0.1923
R_work r_work	0.1903
R_free r_free	0.2299

fit	/app/data/saxs_computation/od/2ody/2ody.fit
pddf	/app/data/pr_computation/od/2ody/2ody.pr.out
profile	/app/data/saxs_computation/od/2ody/2ody.dat

Thrombin-bound boophilin displays a functional and accessible reactive-site loop

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

Prothrombin (EC 3.4.21.5)

State in the Current Structure

Other States of the Same Protein in the Database

Boophilin

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

CATH v4.4 (10 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)