Thrombin
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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 334–622 | Fragment：Heavy and light chain, residues 334-622 | ;Hirudin IIIB' ; × 1 （P28511） NA SODIUM ION × 1 UNB N-(4-CARBAMIMIDOYL-BENZYL)-2-[2-HYDROXY-6-METHYL-3-(NAPHTHALENE-1-SULFONYLAMINO)-PHENYL]-ACETAMIDE × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；27% PEG8000, 0.1M sodium phosphate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K | Resolution 1.61 Å R-free 0.225 |
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 2BDY | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1A2C Structure of thrombin inhibited by AERUGINOSIN298-A from a BLUE-GREEN ALGA Deposited 1997-12-26 | 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 H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.3；pH 7.3
|
Resolution 2.10 Å |
| 1A3B COMPLEX OF HUMAN ALPHA-THROMBIN WITH THE BIFUNCTIONAL BORONATE INHIBITOR BOROLOG1 Deposited 1998-01-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | T29 TRI166 (BIFUNCTIONAL BORONATE INHIBITOR) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.15；20% PEG 8000, 0.05 M SODIUM PHOSPHATE, PH 7.15
|
Resolution 1.80 Å R-free 0.230 |
| 1A3E COMPLEX OF HUMAN ALPHA-THROMBIN WITH THE BIFUNCTIONAL BORONATE INHIBITOR BOROLOG2 Deposited 1998-01-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | T16 BOROLOG2 × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.15；20% PEG 8000, 0.05M SODIUM PHOSPHATE, PH 7.15
|
Resolution 1.85 Å R-free 0.220 |
| 1A46 THROMBIN COMPLEXED WITH HIRUGEN AND A BETA-STRAND MIMETIC INHIBITOR Deposited 1998-02-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 00K (1S,7S)-7-amino-N-[(2R,3S)-7-amino-1-(cyclohexylamino)-2-hydroxy-1-oxoheptan-3-yl]-7-benzyl-8-oxohexahydro-1H-pyrazolo[1,2-a]pyridazine-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion - hanging drop and macroseeding；pH 7.3；0.1 M SODIUM PHOSPHATE BUFFER, PH 7.3, 27-28 % PEG 8000, HANGING DROPS AND MACROSEEDING; THEN SOAKED IN PEG-PHOSPHATE-0.1 M NACL, AND THE MOL 106 INHIBITOR WAS ADDED IN 3 STEPS WITH FINAL CONC. 7.3 MM, vapor diffusion - hanging drop and macroseeding
|
Resolution 2.12 Å |
| 1A4W CRYSTAL STRUCTURES OF THROMBIN WITH THIAZOLE-CONTAINING INHIBITORS: PROBES OF THE S1' BINDING SITE Deposited 1998-02-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 QWE amino{[(4S)-4-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)-5-oxo-5-{(2R)-2-[3-oxo-3-(1,3-thiazol-2-yl)propyl]pip eridin-1-yl}pentyl]amino}methaniminium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion - hanging drop and macroseeding；pH 7.3；0.1 M SODIUM PHOSPHATE BUFFER AT PH 7.3, 27-28% PEG 8000; HANGING DROPS WITH MACROSEEDING, vapor diffusion - hanging drop and macroseeding
|
Resolution 1.80 Å |
| 1A5G HUMAN THROMBIN COMPLEXED WITH NOVEL SYNTHETIC PEPTIDE MIMETIC INHIBITOR AND HIRUGEN Deposited 1998-02-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 00L (1S,7S)-7-amino-7-benzyl-N-[(1S)-4-carbamimidamido-1-{(1S)-1-hydroxy-2-oxo-2-[(2-phenylethyl)amino]ethyl}butyl]-8-oxohexahydro-1H-pyrazolo[1,2-a]pyridazine-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.3；PROTEIN WAS CRYSTALLIZED FROM 15% PEG 8000, 75 MM NAPO4, PH 7.3, 187 MM NACL, 1 MM NAN3; THEN SOAKED IN 7 MM INHIBITOR.
|
Resolution 2.06 Å |
| 1A61 THROMBIN COMPLEXED WITH A BETA-MIMETIC THIAZOLE-CONTAINING INHIBITOR Deposited 1998-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 00N (1S,7S)-7-amino-7-benzyl-N-{(1S)-4-carbamimidamido-1-[(S)-hydroxy(1,3-thiazol-2-yl)methyl]butyl}-8-oxohexahydro-1H-pyra zolo[1,2-a]pyridazine-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion - hanging drop and macroseeding；pH 7.3；THROMBIN-HIRUGEN WAS CRYSTALLIZED FROM 0.1 M SODIUM PHOSPHATE BUFFER AT PH 7.3, 28% PEG 8000 IN HANGING DROPS WITH MACROSEEDING. THE MOL 127 INHIBITOR WAS ADDED BY SOAKING., vapor diffusion - hanging drop and macroseeding
|
Resolution 2.20 Å |
| 1ABI STRUCTURE OF THE HIRULOG 3-THROMBIN COMPLEX AND NATURE OF THE S' SUBSITES OF SUBSTRATES AND INHIBITORS Deposited 1992-08-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å |
| 1ABJ STRUCTURE OF THE HIRULOG 3-THROMBIN COMPLEX AND NATURE OF THE S' SUBSITES OF SUBSTRATES AND INHIBITORS Deposited 1992-08-24 | Different construct Different mutation/modification 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
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.40 Å |
| 1AD8 COMPLEX OF THROMBIN WITH AND INHIBITOR CONTAINING A NOVEL P1 MOIETY Deposited 1997-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 |
| 1AE8 HUMAN ALPHA-THROMBIN INHIBITION BY EOC-D-PHE-PRO-AZALYS-ONP Deposited 1997-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 AZL 1-ETHOXYCARBONYL-D-PHE-PRO-2(4-AMINOBUTYL)HYDRAZINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；277 K；PEG 4000 15%, PH 7.0, 5X10-3 M AZALYS-DERIVATIVE, 277 K.
|
Resolution 2.00 Å |
| 1AFE HUMAN ALPHA-THROMBIN INHIBITION BY CBZ-PRO-AZALYS-ONP Deposited 1997-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ALZ 2-[N'-(4-AMINO-BUTYL)-HYDRAZINOCARBONYL]-PYRROLIDINE-1-CARBOXYLIC ACID BENZYL ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；PEG 4000 15%, PH 7.0, 5X10-3 M AZALYS COMPOUND
|
Resolution 2.00 Å |
| 1AHT CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN COMPLEXED WITH HIRUGEN AND P-AMIDINOPHENYLPYRUVATE AT 1.6 ANGSTROMS RESOLUTION Deposited 1995-03-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | APA (2S)-3-(4-carbamimidoylphenyl)-2-hydroxypropanoic acid × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.60 Å |
| 1AI8 HUMAN ALPHA-THROMBIN TERNARY COMPLEX WITH THE EXOSITE INHIBITOR HIRUGEN AND ACTIVE SITE INHIBITOR PHCH2OCO-D-DPA-PRO-BOROMPG Deposited 1997-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | T42 MORPHOLINO-DIPHENYLALANINE-METHOXYPROPYLBORONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.2；277 K；PROTEIN COMPLEX WAS CRYSTALLIZED FROM 25% PEG 8000 0.05 SODIUM PHOSPHATE, PH 7.2, TEMPERATURE 277 K.
|
Resolution 1.85 Å R-free 0.240 |
| 1AIX HUMAN ALPHA-THROMBIN TERNARY COMPLEX WITH EXOSITE INHIBITOR HIRUGEN AND ACTIVE SITE INHIBITOR PHCH2OCO-D-DPA-PRO-BOROVAL Deposited 1997-04-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | T19 PHENYLMETHYLENECARBOXY-(METHYLENEAMINO-FORMYL-DIPHENYLMETHYL)METHY-PRO-BOROVAL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.2；277 K；PROTEIN WAS CRYSTALLIZED FROM 25% PEG 8000, 0.05M SODIUM PHOSPHATE, PH 7.2, TEMPERATURE 4 DEGREES CELSIUS, temperature 277K
|
Resolution 2.10 Å R-free 0.230 |
| 1AWF NOVEL COVALENT THROMBIN INHIBITOR FROM PLANT EXTRACT Deposited 1997-10-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | GR4 R3-ACETOXY-17-(1-FORMYL-5-METHYL-3-OXO-HEX-4-ENYL)-12,16-DIHYDROXY-14-HYDROXYMETHYL-4,10,13-TRIMETHYL-2,3,4,5,6,9,10,11,12,13,14,15,16,17-TETRADECAHYDRO-1H-CYCLOPENTA[A]PHENANTHRENE-4-CARBOXYLIC ACID IDOPYRANOSYL ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；CRYSTALS WERE GROWN BY MACROSEEDING A SOLUTION OF 100MM HEPES PH 7.0, 22% PEG4K, 200MM NACL. THE SOLUTION CONTAINED 25%DMSO. PROTEIN CONCENTRATION OF 5MG/ML.
|
Resolution 2.20 Å |
| 1AWH NOVEL COVALENT THROMBIN INHIBITOR FROM PLANT EXTRACT Deposited 1997-10-02 | Different construct Different mutation/modification 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
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | GR3 3-ACETOXY-17-(1-FORMYL-5-METHYL-3-OXO-HEX-4-ENYL)-16-HYDROXY-4,10,13,14-TETRAMETHYL-2,3,4,5,6,9,10,11,12,13,14,15,16,17-TETRADECAHYDRO-1H-CYCLOPENTA[A]PHENANTHRENE-4-CARBOXYLIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4；14% PEG4K, 100MM NA ACETATE, PH 4.0.
|
Resolution 3.00 Å |
| 1AWH NOVEL COVALENT THROMBIN INHIBITOR FROM PLANT EXTRACT Deposited 1997-10-02 | Different construct Different mutation/modification 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
328–363（36 aa）
Chain D
364–622（259 aa）
|
Not recorded | GR3 3-ACETOXY-17-(1-FORMYL-5-METHYL-3-OXO-HEX-4-ENYL)-16-HYDROXY-4,10,13,14-TETRAMETHYL-2,3,4,5,6,9,10,11,12,13,14,15,16,17-TETRADECAHYDRO-1H-CYCLOPENTA[A]PHENANTHRENE-4-CARBOXYLIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4；14% PEG4K, 100MM NA ACETATE, PH 4.0.
|
Resolution 3.00 Å |
| 1AY6 THROMBIN INHIBITOR FROM THEONALLA, CYCLOTHEANAMIDE-BASED MACROCYCLIC TRIPEPTIDE MOTIF Deposited 1997-11-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 |
| 1B5G HUMAN THROMBIN COMPLEXED WITH NOVEL SYNTHETIC PEPTIDE MIMETIC INHIBITOR AND HIRUGEN Deposited 1998-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 0ZE [[[(4S,5S)-4-[[(3S,6S,8aR)-6-azanyl-5-oxo-6-(phenylmethyl)-1,2,3,7,8,8a-hexahydroindolizin-3-yl]carbonylamino]-5-(1,3-b enzothiazol-2-yl)-5-hydroxy-pentyl]amino]-azanyl-methylidene]azanium × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.3；PROTEIN WAS CRYSTALLIZED FROM 15% PEG 8000, 75 MM NAPO4, PH 7.3, 187 MM NACL, 1 MM NAN3; THEN SOAKED IN 7 MM INHIBITOR.
|
Resolution 2.07 Å |
| 1B7X STRUCTURE OF HUMAN ALPHA-THROMBIN Y225I MUTANT BOUND TO D-PHE-PRO-ARG-CHLOROMETHYLKETONE Deposited 1999-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Mutation：Y225I | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；pH 7.5
|
Resolution 2.10 Å R-free 0.282 |
| 1BA8 THROMBIN INHIBITOR WITH A RIGID TRIPEPTIDYL ALDEHYDES Deposited 1998-04-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | 0IT amino({(4S)-4-[({(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}acetyl)amino]-5-oxopentyl}amino)methaniminium × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；pH 7.5
|
Resolution 1.80 Å |
| 1BB0 THROMBIN INHIBITORS WITH RIGID TRIPEPTIDYL ALDEHYDES Deposited 1998-04-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | NA SODIUM ION × 2 0IV 2-{(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}-N-{(2S)-1-[(3R)-1-carbamimidoylpiperidin-3-yl]-3-oxopropan-2-yl}acetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；pH 7.5
|
Resolution 2.10 Å |
| 1BCU ALPHA-THROMBIN COMPLEXED WITH HIRUGEN AND PROFLAVIN Deposited 1998-05-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | PRL PROFLAVIN × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；pH 7
|
Resolution 2.00 Å R-free 0.212 |
| 1BHX X-RAY STRUCTURE OF THE COMPLEX OF HUMAN ALPHA THROMBIN WITH THE INHIBITOR SDZ 229-357 Deposited 1998-06-10 | 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 A
331–360（30 aa）
Chain B
364–510（147 aa）
Chain F
518–622（105 aa）
|
Not recorded | R56 5-OXO-6-PHENYLMETHANESULFONYLAMINO-HEXAHYDRO-THIAZOLO[3,2-A]PYRIDINE-3-CARBOXYLIC ACID (3-GUANIDINO-PROPYL)-AMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.3；pH 7.3
|
Resolution 2.30 Å R-free 0.232 |
| 1BMM HUMAN ALPHA-THROMBIN COMPLEXED WITH [S-(R*,R*)]-4-[(AMINOIMINOMETHYL)AMINO]-N-[[1-[3-HYDROXY-2-[(2-NAPHTHALENYLSULFONYL)AMINO]-1-OXOPROPYL]-2-PYRROLIDINYL] METHYL]BUTANAMIDE (BMS-186282) Deposited 1995-11-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | BM2 S-(R*,R*)]-4-[AMINOIMINOMETHYL)AMINO]-N-[[1-[3-HYDROXY -2-[(2-NAPHTHALENYLSULFONYL)AMINO]-1-OXOPROPYL]-2-PYRROLIDINYL] METHYL]BUTANAMIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.60 Å |
| 1BMN HUMAN ALPHA-THROMBIN COMPLEXED WITH [S-(R*,R*)]-1-(AMINOIMINOMETHYL)-N-[[1-[N-[(2-NAPHTHALENYLSULFONYL)-L-SERYL]-PYRROLIDINYL]METHYL]-3-PIPERIDENECARBOXAMIDE (BMS-189090) Deposited 1995-11-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | BM9 [S-(R*,R*)]-1-(AMINOIMINOMETHYL)-N-[[1-[N-[(2-NAPHTHALENYLSULFONYL)-L-SERYL]-3-PYRROLIDINYL]METHYL]-3-PIPERIDENECARBOXA MIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.80 Å |
| 1BTH STRUCTURE OF THROMBIN COMPLEXED WITH BOVINE PANCREATIC TRYPSIN INHIBITOR Deposited 1996-12-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Mutation：E192Q Mutation：E192Q | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å R-free 0.271 |
| 1BTH STRUCTURE OF THROMBIN COMPLEXED WITH BOVINE PANCREATIC TRYPSIN INHIBITOR Deposited 1996-12-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain J
328–363（36 aa）
Chain K
364–622（259 aa）
|
Mutation：E192Q Mutation：E192Q | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å R-free 0.271 |
| 1C1U RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES Deposited 1999-07-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：HEAVY CHAIN
Chain L
328–363（36 aa）
Fragment：LIGHT CHAIN
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 1 BAI (5-AMIDINO-2-BENZIMIDAZOLYL)(2-BENZIMIDAZOLYL)METHANE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.2；THROMBIN WAS PURCHASED FROM HAEMATOLOGIC TECHNOLOGIES, INC. AND ACETYL-HIRUDIN
FROM BACHEM. THROMBIN WAS PREPARED AS DESCRIBED (SKRZPCZAK-JANKUN ET AL., 1991)
.THROMBIN (1.0 MG/ML IN 50 MM HEPES, 50 % GLYCEROL, PH 7.0) WAS INCUBATED
WITH 1.0 MM ACETYL-HIRUDIN, 1.0 MM HEMI-BABIM, 1.0 MM ZN+2 FOR 1 HR AT 4 DEG
C. GLYCEROL WAS REMOVED AND THE COMPLEX CONCENTRATED WITH A CENTRICON 10 (
AMICON) TO 8.6 MG/ML AS DETERMINED BY THE BIORAD PROTEIN ASSAY KIT USING
BOVINE SERUM ALBUMIN. CRYSTALS OF THROMBIN-ACETYL-HIRUDIN-HEMI-BABIM-ZN+2 WERE
GROWN IN HANGING DROPS BY VAPOR DIFFUSION AFTER STREAK SEEDING. THE DROPS WERE
MADE FROM 5 MICROLITERS OF COMPLEX AND 5 MICROLITERS OF RESERVOIR SOLUTION (
0.10 M TRIS,0.50 M NACL, 22 % (BY VOLUME) PEG 4K, PH 8.20).
|
Resolution 1.75 Å R-free 0.235 |
| 1C1V RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES Deposited 1999-07-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | ZN ZINC ION × 2 NA SODIUM ION × 1 BAB BIS(5-AMIDINO-BENZIMIDAZOLYL)METHANE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；THROMBIN WAS PURCHASED FROM HAEMATOLOGIC TECHNOLOGIES, INC. AND ACETYL-HIRUDIN
FROM BACHEM. THROMBIN WAS PREPARED AS DESCRIBED (SKRZPCZAK-JANKUN ET AL., 1991)
.THROMBIN (1.0 MG/ML IN 50 MM HEPES, 50 % GLYCEROL, PH 7.0) WAS INCUBATED
WITH 1.0 MM ACETYL-HIRUDIN, 1.0 MM BABIM, 1.0 MM ZN+2 FOR 1 HR AT 4 DEG C.
GLYCEROL WAS REMOVED AND THE COMPLEX CONCENTRATED WITH A CENTRICON 10 (AMICON)
TO 8.6 MG/ML AS DETERMINED BY THE BIORAD PROTEIN ASSAY KIT USING BOVINE SERUM
ALBUMIN. CRYSTALS OF THROMBIN-ACETYL-HIRUDIN-BABIM-ZN+2 WERE GROWN IN HANGING
DROPS BY VAPOR DIFFUSION AFTER STREAK SEEDING. THE DROPS WERE MADE FROM 5
MICROLITERS OF COMPLEX AND 5 MICROLITERS OF RESERVOIR SOLUTION (0.10 M TRIS,
0.50 M NACL, 22 % (BY VOLUME) PEG 4K, PH 7.00). A CO-CRYSTAL WAS SOAKED IN 30 %
PEG 4K,0.50 M NACL, 0.10 M TRIS, 46 MM ZN+2, PH 7.00, SATURATED IN BABIM AND
CONTAINING 2 % DMSO.
|
Resolution 1.98 Å R-free 0.248 |
| 1C1W RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES Deposited 1999-07-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | ZN ZINC ION × 3 NA SODIUM ION × 1 BAH BIS(5-AMIDINO-2-BENZIMIDAZOLYL)METHANE KETONE HYDRATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 9；THROMBIN WAS PURCHASED FROM HAEMATOLOGIC TECHNOLOGIES, INC. AND ACETYL-HIRUDIN
FROM BACHEM. THROMBIN WAS PREPARED AS DESCRIBED (SKRZPCZAK-JANKUN ET AL., 1991)
.THROMBIN (1.0 MG/ML IN 50 MM HEPES, 50 % GLYCEROL, PH 7.0) WAS INCUBATED
WITH 1.0 MM ACETYL-HIRUDIN, 1.0 MM BABIM, 1.0 MM ZN+2 FOR 1 HR AT 4 DEG C.
GLYCEROL WAS REMOVED AND THE COMPLEX CONCENTRATED WITH A CENTRICON 10 (AMICON)
TO 8.6 MG/ML AS DETERMINED BY THE BIORAD PROTEIN ASSAY KIT USING BOVINE SERUM
ALBUMIN. CRYSTALS OF THROMBIN-ACETYL-HIRUDIN-BABIM-ZN+2 WERE GROWN IN HANGING
DROPS BY VAPOR DIFFUSION AFTER STREAK SEEDING. THE DROPS WERE MADE FROM 5
MICROLITERS OF COMPLEX AND 5 MICROLITERS OF RESERVOIR SOLUTION (0.10 M TRIS,
0.50 M NACL, 22 % (BY VOLUME) PEG 4K, PH 7.00). A CO-CRYSTAL WAS SOAKED IN 30 %
PEG 4K,0.50 M NACL, 0.10 M TRIS, 0.4 MM ZN+2, PH 9.00, SATURATED IN KETO-
BABIM AND CONTAINING 2 % DMSO.
|
Resolution 1.90 Å R-free 0.242 |
| 1C4U SELECTIVE NON ELECTROPHILIC THROMBIN INHIBITORS WITH CYCLOHEXYL MOIETIES. Deposited 1999-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain 1
328–363（36 aa）
Chain 2
364–622（259 aa）
|
Not recorded | NA SODIUM ION × 1 IH1 2-[2-(4-BROMO-BENZENESULFONYL)-ETHYL]-1-3-DIOXO-2,3,5,8-TETRAHYDRO-1H-[1,2,4]TRIAZOLO[1,2-A]PYRIDAZINE-5-CARBOXYLIC ACID(4-CARBAMIMIDOYL-CYCLOHEXYLMETHYL)-AMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；pH 7.5
|
Resolution 2.10 Å |
| 1C4V SELECTIVE NON ELECTROPHILIC THROMBIN INHIBITORS WITH CYCLOHEXYL MOIETIES. Deposited 1999-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain 1
328–363（36 aa）
Chain 2
364–622（259 aa）
|
Not recorded | NA SODIUM ION × 1 IH2 2-(2,2-DIPHENYL-ETHYL)-7-METHYL-1,3-DIOXO-2,3,5,8-TETRAHYDRO-1H-[1,2,4]TRIAZOLO [1,2-A]PYRIDAZINE-5-CARBOXYLIC ACID(4-CARBAMIMIDOYL-CYCLOHEXYLMETHYL)-AMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；pH 7.5
|
Resolution 2.10 Å |
| 1C4Y SELECTIVE NON-ELECTROPHILIC THROMBIN INHIBITORS Deposited 1999-10-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain 1
328–363（36 aa）
Chain 2
364–622（259 aa）
|
Not recorded | IH3 2-(2,2-DIPHENYL-ETHYL)-7-METHYL-1,3-DIOXO-2,3,5,8-TETRAHYDRO-1H-[1,2,4] TRIAZOLO[1,2-A]PYRIDAZINE-5-CARBOXYLIC ACID [4-(2-AMINO-3H-IMIDAZOL-4-YL)-CYCLOHEXYL]-AMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；pH 7.5
|
Resolution 2.70 Å |
| 1C5L STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR Deposited 1999-12-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：HEAVY CHAIN
Chain L
328–363（36 aa）
Fragment：LIGHT CHAIN
|
Not recorded | NA SODIUM ION × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.2；Thrombin was purchased from Haematologic Technologies, Inc.
and acetyl-hirudin from Bachem. Thrombin was prepared as described
(Skrzpczak-Jankun et al., 1991). Thrombin (1.0 mg/ml in 50 mM HEPES, 50 %
glycerol, pH 7.0) was incubated with 1.0 mM acetyl-hirudin for 1 hr at
4 deg C. Glycerol was removed and the complex concentrated with a
centricon 10 (Amicon) to about 10 mg/ml as determined by the Biorad protein
assay kit using bovine serum albumin. Crystals of thrombin-acetyl-hirudin
were grown in hanging drops by vapor diffusion after streak seeding. The
drops were made from 5 microliters of complex and 5 microliters of reservoir
solution (0.10 M Tris, 0.50 M NaCl, 22 % (by volume) PEG 4K, pH 8.20)., VAPOR DIFFUSION
|
Resolution 1.47 Å R-free 0.236 |
| 1C5N STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR Deposited 1999-12-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 1 CA CALCIUM ION × 1 ESI 4-IODOBENZO[B]THIOPHENE-2-CARBOXAMIDINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；Thrombin was purchased from Haematologic Technologies,
Inc. and acetyl-hirudin from Bachem. Thrombin was prepared as
described (Skrzpczak-Jankun et al., 1991).
Thrombin (1.0 mg/ml in 50 mM HEPES, 50 % glycerol, pH 7.0)
was incubated with 1.0 mM acetyl-hirudin, 10 mM
4-iodobenzo[b]thiophene-2-carboxamidine for 1 hr at 4 deg C.
Glycerol was removed andthe complex concentrated with a
centricon 10 (Amicon) to about 10 mg/ml as determined by
the Biorad protein assay kit using bovine serum albumin.
Crystals of thrombin-acetyl-hirudin-4-iodobenzo[b]thiophene-2-carboxamidine
were grown in hanging drops by vapor diffusion after
streak seeding. The drops were made from 5 microliters of
complex and 5 microliters of reservoir solution
(0.10 M Tris,0.50 M NaCl, 22 % (by volume) PEG 4K, pH 7.5)., VAPOR DIFFUSION
|
Resolution 1.50 Å R-free 0.246 |
| 1C5O STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR Deposited 1999-12-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：HEAVY CHAIN
Chain L
328–363（36 aa）
Fragment：LIGHT CHAIN
|
Not recorded | NA SODIUM ION × 1 BEN BENZAMIDINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；Thrombin was purchased from Haematologic Technologies,
Inc. and acetyl-hirudin from Bachem.
Thrombin was prepared as described (Skrzpczak-Jankun et al., 1991).
Thrombin (1.0 mg/ml in 50 mM HEPES, 50 % glycerol, pH 7.0) was
incubated with 1.0 mM acetyl-hirudin, 10 mM benzamidine for 1 hr
at 4 deg C. Glycerol was removed and the complex concentrated
with a centricon 10 (Amicon) to about 10 mg/ml as determined by the
Biorad protein assay kit using bovine serum albumin. Crystals of
thrombin-acetyl-hirudin-benzmaidine were grown in hanging drops
by vapor diffusion after streak seeding. The drops were made
from 5 microliters of complex and 5 microliters of reservoir
solution (0.10 M Tris, 0.50 M NaCl, 22 % (by volume) PEG 4K, pH 7.5)., VAPOR DIFFUSION
|
Resolution 1.90 Å R-free 0.262 |
| 1CA8 Thrombin inhibitors with rigid tripeptidyl aldehydes Deposited 1998-04-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：Peptidase S1 domain
Chain B
364–622（259 aa）
|
Not recorded | NA SODIUM ION × 2 0KV 2-{(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}-N-{(2S)-1-[(3S)-1-carbamimidoylpiperidin-3-yl]-3-oxopropan-2-yl}acetamide × 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 2.10 Å |
| 1CGL Structure of the catalytic domain of fibroblast collagenase complexed with an inhibitor Deposited 1993-11-17 | Different construct 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
101–269（169 aa）
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 1 0ED N-[(1S)-3-{[(benzyloxy)carbonyl]amino}-1-carboxypropyl]-L-leucyl-N-(2-morpholin-4-ylethyl)-L-phenylalaninamide × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.40 Å |
| 1CGL Structure of the catalytic domain of fibroblast collagenase complexed with an inhibitor Deposited 1993-11-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
101–269（169 aa）
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 1 0ED N-[(1S)-3-{[(benzyloxy)carbonyl]amino}-1-carboxypropyl]-L-leucyl-N-(2-morpholin-4-ylethyl)-L-phenylalaninamide × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.40 Å |
| 1D3D CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZOTHIOPHENE INHIBITOR 4 Deposited 1999-09-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–360（28 aa）
Chain B
364–620（257 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 BZT 3-(3-BROMO-4-PYRROLIDIN-1-YLMETHYL-BENZYL)-2-[4-PYRROLIDIN-1-YL-ETHOXY)-PHENYL]-BENZO[B]THIOPHEN-6-OL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；30% PEG 3400, 100MM SODIUM CITRATE, 200 MM AMMONIUM ACETATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.04 Å R-free 0.223 |
| 1D3P CRYSTAL STRUCTURE OF HUMAN APLHA-THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE INHIBITOR 3 Deposited 1999-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：LIGHT CHAIN
Chain B
364–622（259 aa）
Fragment：HEAVY CHAIN
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 BT3 3-[4-(2-PYRROLIDIN-1-YL-ETHOXY)-BENZYL]-2-4-(2-PYRROLIDIN-1-YL-ETHOXY)-PHENYL] -BENZO[B]THIOPHEN-6-OL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；30% PEG3400; 100mM sodium citrate; 200 mM ammonium acetate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.10 Å R-free 0.214 |
| 1D3Q CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE INHIBITOR 2 Deposited 1999-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 BT2 3-[4-(2-PYRROLIDIN-1-YL-ETHOXY)-BENZYL]-2-4-(2-PYRROLIDIN-1-YL-ETHOXY)-PHENYL] -BENZO[B]THIOPHENE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；30% PEG3400; 100 mM sodium citrate; 200 mM ammonium acetate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.90 Å R-free 0.228 |
| 1D3T CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE INHIBITOR 1 Deposited 1999-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：LIGHT CHAIN
Chain B
364–622（259 aa）
Fragment：HEAVY CHAIN
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 BT1 {2-[4-(2-PYRROLIDIN-1-YL-ETHOXY)-PHENYL]-BENZO[B]THIOPHEN-3-YL}-[4-(2-PYRROLIDIN-1-YL-ETHOXY)-PHENYL]-METHANONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；30% PEG 3400; 100 mM sodium citrate; 200 mM ammonium acetate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 3.00 Å R-free 0.235 |
| 1D4P CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH 5-AMIDINOINDOLE-4-BENZYLPIPERIDINE INHIBITOR Deposited 1999-10-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：LIGHT CHAIN
Chain B
364–622（259 aa）
Fragment：HEAVY CHAIN
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 BPP 2-(4-benzylpiperidine-1-carbonyl)-1H-indole-5-carboximidamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.6；277 K；30% PEG 4000, 150 mM sodium citrate, 200 mM ammonium acetate, pH 5.6, VAPOR DIFFUSION, temperature 277K
|
Resolution 2.07 Å R-free 0.231 |
| 1D6W STRUCTURE OF THROMBIN COMPLEXED WITH SELECTIVE NON-ELECTROPHILIC INHIBITORS HAVING CYCLOHEXYL MOIETIES AT P1 Deposited 1999-10-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
334–620（287 aa）
|
Not recorded | NA SODIUM ION × 2 00R (5S)-N-[trans-4-(2-amino-1H-imidazol-5-yl)cyclohexyl]-1,3-dioxo-2-[2-(phenylsulfonyl)ethyl]-2,3,5,8-tetrahydro-1H-[1,2,4]triazolo[1,2-a]pyridazine-5-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；24% PEG 8000, 0.1M Sodium Phosphate buffer,
Protein concentration: 3.5 mg/ml, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å |
| 1D9I STRUCTURE OF THROMBIN COMPLEXED WITH SELECTIVE NON-ELECTOPHILIC INHIBITORS HAVING CYCLOHEXYL MOIETIES AT P1 Deposited 1999-10-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
334–621（288 aa）
|
Not recorded | NA SODIUM ION × 2 00P (5S)-N-[(trans-4-aminocyclohexyl)methyl]-1,3-dioxo-2-[2-(phenylsulfonyl)ethyl]-2,3,5,8-tetrahydro-1H-[1,2,4]triazolo[1,2-a]pyridazine-5-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；24% PEG 8000 in 0.1M Sodium Phosphate Buffer, protein concentration: 3.5 mg/ml, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.30 Å |
| 1DE7 INTERACTION OF FACTOR XIII ACTIVATION PEPTIDE WITH ALPHA-THROMBIN: CRYSTAL STRUCTURE OF THE ENZYME-SUBSTRATE COMPLEX Deposited 1999-11-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；PEG8000, SODIUM CHLORIDE, SODIUM CITRATE, pH 5.50
|
Resolution 2.00 Å R-free 0.257 |
| 1DE7 INTERACTION OF FACTOR XIII ACTIVATION PEPTIDE WITH ALPHA-THROMBIN: CRYSTAL STRUCTURE OF THE ENZYME-SUBSTRATE COMPLEX Deposited 1999-11-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain J
328–363（36 aa）
Chain K
364–622（259 aa）
|
Not recorded | NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；PEG8000, SODIUM CHLORIDE, SODIUM CITRATE, pH 5.50
|
Resolution 2.00 Å R-free 0.257 |
| 1DIT COMPLEX OF A DIVALENT INHIBITOR WITH THROMBIN Deposited 1995-07-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å |
| 1DM4 SER195ALA MUTANT OF HUMAN THROMBIN COMPLEXED WITH FIBRINOPEPTIDE A (7-16) Deposited 1999-12-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–362（35 aa）
Chain B
363–622（260 aa）
|
Mutation：S195A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；1.4M SODIUM CITRATE, 1-2% ISOPROPANOL, 0.1M HEPES BUFFER, pH 7.50
|
Resolution 2.50 Å |
| 1DM4 SER195ALA MUTANT OF HUMAN THROMBIN COMPLEXED WITH FIBRINOPEPTIDE A (7-16) Deposited 1999-12-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
328–362（35 aa）
Chain B
363–622（260 aa）
|
Mutation：S195A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；1.4M SODIUM CITRATE, 1-2% ISOPROPANOL, 0.1M HEPES BUFFER, pH 7.50
|
Resolution 2.50 Å |
| 1DOJ Crystal structure of human alpha-thrombin*RWJ-51438 complex at 1.7 A Deposited 1999-12-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
328–622（295 aa）
|
Not recorded | 1Z0 N-methyl-D-phenylalanyl-N-{(1S)-4-carbamimidamido-1-[(6-carboxy-1,3-benzothiazol-2-yl)carbonyl]butyl}-L-prolinamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.75 sodium acetate, 0.01% (w/v), 20% polyethylene glycol 4000 (w/v), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
|
Resolution 1.70 Å R-free 0.217 |
| 1DWB CRYSTALLOGRAPHIC ANALYSIS AT 3.0-ANGSTROMS RESOLUTION OF THE BINDING TO HUMAN THROMBIN OF FOUR ACTIVE SITE-DIRECTED INHIBITORS Deposited 1992-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | BEN BENZAMIDINE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.16 Å |
| 1DWC CRYSTALLOGRAPHIC ANALYSIS AT 3.0-ANGSTROMS RESOLUTION OF THE BINDING TO HUMAN THROMBIN OF FOUR ACTIVE SITE-DIRECTED INHIBITORS Deposited 1992-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 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 3.00 Å |
| 1DWD CRYSTALLOGRAPHIC ANALYSIS AT 3.0-ANGSTROMS RESOLUTION OF THE BINDING TO HUMAN THROMBIN OF FOUR ACTIVE SITE-DIRECTED INHIBITORS Deposited 1992-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 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 3.00 Å |
| 1DWE Crystallographic analysis at 3.0-Angstroms resolution of the binding to human thrombin of four active site-directed inhibitors Deposited 1992-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.00 Å |
| 1DX5 Crystal structure of the thrombin-thrombomodulin complex Deposited 1999-12-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: tetrameric |
Chain A
328–363（36 aa）
Chain M
364–622（259 aa）
|
Not recorded | FMT FORMIC ACID × 1 CA CALCIUM ION × 1 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；0.1 M NA ACETATE (PH 4.6), 1.8 M NA FORMATE, 0.002 M CA CHLORIDE
|
Resolution 2.30 Å R-free 0.241 |
| 1DX5 Crystal structure of the thrombin-thrombomodulin complex Deposited 1999-12-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: tetrameric |
Chain B
328–363（36 aa）
Chain N
364–622（259 aa）
|
Not recorded | FMT FORMIC ACID × 1 CA CALCIUM ION × 1 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；0.1 M NA ACETATE (PH 4.6), 1.8 M NA FORMATE, 0.002 M CA CHLORIDE
|
Resolution 2.30 Å R-free 0.241 |
| 1DX5 Crystal structure of the thrombin-thrombomodulin complex Deposited 1999-12-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: tetrameric |
Chain C
328–363（36 aa）
Chain O
364–622（259 aa）
|
Not recorded | FMT FORMIC ACID × 1 CA CALCIUM ION × 1 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；0.1 M NA ACETATE (PH 4.6), 1.8 M NA FORMATE, 0.002 M CA CHLORIDE
|
Resolution 2.30 Å R-free 0.241 |
| 1DX5 Crystal structure of the thrombin-thrombomodulin complex Deposited 1999-12-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: tetrameric |
Chain D
328–363（36 aa）
Chain P
364–622（259 aa）
|
Not recorded | FMT FORMIC ACID × 2 CA CALCIUM ION × 1 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；0.1 M NA ACETATE (PH 4.6), 1.8 M NA FORMATE, 0.002 M CA CHLORIDE
|
Resolution 2.30 Å R-free 0.241 |
| 1E0F Crystal structure of the human alpha-thrombin-haemadin complex: an exosite II-binding inhibitor Deposited 2000-03-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
328–363（36 aa）
Chain B
328–363（36 aa）
Chain C
328–363（36 aa）
Chain D
364–622（259 aa）
Fragment：NO
Chain E
364–622（259 aa）
Fragment：NO
Chain F
364–622（259 aa）
Fragment：NO
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.56；VAPOUR-DIFFUSION SITTING DROP,0.1 M NA CITRATE PH 5.56 14% (W/V) PEG4000, 12.5% (V/V) ISOPROPANOL
|
Resolution 3.10 Å R-free 0.255 |
| 1EB1 Complex structure of human thrombin with N-methyl-arginine inhibitor Deposited 2001-07-18 | 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 H
364–620（257 aa）
Chain L
334–360（27 aa）
Fragment：CATALYTIC DOMAIN RESIDUES 364-620
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；PH 8.00
|
Resolution 1.80 Å R-free 0.220 |
| 1EOJ Design of P1' and P3' residues of trivalent thrombin inhibitors and their crystal structures Deposited 2000-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
332–620（289 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；PEG 4000, Potassium sulfate, citric acid pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.10 Å R-free 0.233 |
| 1EOL Design of P1' and P3' residues of trivalent thrombin inhibitors and their crystal structures Deposited 2000-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
332–620（289 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；PEG 4000, Potassium sulfate, citric acid pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.10 Å R-free 0.240 |
| 1FPC ACTIVE SITE MIMETIC INHIBITION OF THROMBIN Deposited 1994-10-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 0ZI amino{[(4S)-4-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)-5-(4-ethylpiperidin-1-yl)-5-oxopentyl]amino}methaniminium × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å |
| 1FPH THE INTERACTION OF THROMBIN WITH FIBRINOGEN: A STRUCTURAL BASIS FOR ITS SPECIFICITY Deposited 1993-04-21 | 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 H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.50 Å |
| 1G30 THROMBIN INHIBITOR COMPLEX Deposited 2000-10-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：LIGHT CHAIN
Chain B
364–622（259 aa）
Fragment：HEAVY CHAIN
|
Not recorded | T87 [(1-{2[(4-CARBAMIMIDOYL-PHENYLAMINO)-METHYL]-1-METHYL-1H-BENZOIMIDAZOL-5-YL}-CYCLOPROPYL)-PYRIDIN-2-YL-METHYLENEAMINOOXY]-ACETIC ACID ETHYL ESTER × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.00 Å R-free 0.264 |
| 1G32 THROMBIN INHIBITOR COMPLEX Deposited 2000-10-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：LIGHT CHAIN
Chain B
364–622（259 aa）
Fragment：HEAVY CHAIN
|
Not recorded | R11 4-{[1-METHYL-5-(2-METHYL-BENZOIMIDAZOL-1-YLMETHYL)-1H-BENZOIMIDAZOL-2-YLMETHYL]-AMINO}-BENZAMIDINE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.90 Å R-free 0.289 |
| 1G37 CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN COMPLEXED WITH BCH-10556 AND EXOSITE-DIRECTED PEPTIDE Deposited 2000-10-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
334–620（287 aa）
|
Not recorded | 110 3-(4-AMINO-CYCLOHEXYL)-2-HYDROXY-3-[(4-OXO-2-PHENYLMETHANESULFONYL-1,2,3,4-TETRAHYDRO-PYRROLO[1,2-A]PYRAZINE-6-CARBONYL)-AMINO]-PROPIONIC ACID BUTYL ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；296 K；PEG 8000, sodium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 296K, temperature 296.0K
|
Resolution 2.00 Å R-free 0.248 |
| 1GHV A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE Deposited 2001-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Fragment：HEAVY CHAIN, RESIDUES 364-620
Chain L
328–363（36 aa）
Fragment：LIGHT CHAIN, RESIDUES 328-363
|
Not recorded | NA SODIUM ION × 1 120 2-(2-OXO-1,2-DIHYDRO-PYRIDIN-3-YL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.8；298 K；PEG 4000, NaCl, pH 7.8, vapor diffusion, temperature 298K
|
Resolution 1.85 Å R-free 0.235 |
| 1GHW A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE Deposited 2001-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Fragment：HEAVY CHAIN, RESIDUES 364-620
Chain L
328–363（36 aa）
Fragment：LIGHT CHAIN, RESIDUES 328-363
|
Not recorded | NA SODIUM ION × 1 BMZ 2-(2-HYDROXY-PHENYL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.3；298 K；PEG 4000, NaCl, pH 7.3, vapor diffusion, temperature 298K
|
Resolution 1.75 Å R-free 0.234 |
| 1GHX A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE Deposited 2001-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Fragment：HEAVY CHAIN, RESIDUES 364-620
Chain L
328–363（36 aa）
Fragment：LIGHT CHAIN, RESIDUES 328-363
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 BMZ 2-(2-HYDROXY-PHENYL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.3；298 K；PEG 4000, NaCl (soak at pH 8.2), pH 7.3, vapor diffusion, temperature 298K
|
Resolution 1.65 Å R-free 0.255 |
| 1GHY A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE Deposited 2001-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Fragment：HEAVY CHAIN, RESIDUES 364-620
Chain L
328–363（36 aa）
Fragment：LIGHT CHAIN, RESIDUES 328-363
|
Not recorded | ZN ZINC ION × 3 NA SODIUM ION × 1 CA CALCIUM ION × 1 121 2-(3-HYDROXY-PYRIDIN-2-YL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.2；298 K；PEG 4000, NaCl, pH 8.2, vapor diffusion, temperature 298K
|
Resolution 1.85 Å R-free 0.220 |
| 1GHY A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE Deposited 2001-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain H
364–620（257 aa）
Fragment：HEAVY CHAIN, RESIDUES 364-620
Chain L
328–363（36 aa）
Fragment：LIGHT CHAIN, RESIDUES 328-363
|
Not recorded | ZN ZINC ION × 6 NA SODIUM ION × 2 CA CALCIUM ION × 2 121 2-(3-HYDROXY-PYRIDIN-2-YL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.2；298 K；PEG 4000, NaCl, pH 8.2, vapor diffusion, temperature 298K
|
Resolution 1.85 Å R-free 0.220 |
| 1GJ4 SELECTIVITY AT S1, H2O DISPLACEMENT, UPA, TPA, SER190/ALA190 PROTEASE, STRUCTURE-BASED DRUG DESIGN Deposited 2001-04-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Fragment：HEAVY CHAIN, RESIDUES 364-620
Chain L
328–363（36 aa）
Fragment：LIGHT CHAIN, RESIDUES 328-363
|
Not recorded | NA SODIUM ION × 1 132 6-CHLORO-2-(2-HYDROXY-BIPHENYL-3-YL)-1H-INDOLE-5-CARBOXAMIDINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.8；298 K；PEG 4000, NaCl (soak at pH 9.0), vapor diffusion at 298K, pH 7.8
|
Resolution 1.81 Å R-free 0.236 |
| 1GJ5 SELECTIVITY AT S1, H2O DISPLACEMENT, UPA, TPA, SER190/ALA190 PROTEASE, STRUCTURE-BASED DRUG DESIGN Deposited 2001-04-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Fragment：HEAVY CHAIN, RESIDUES 364-620
Chain L
328–363（36 aa）
Fragment：LIGHT CHAIN, RESIDUES 328-363
|
Not recorded | NA SODIUM ION × 1 130 2-(2-HYDROXY-BIPHENYL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.3；298 K；PEG 4000, NaCl (soak at pH 8.68), vapor diffusion at 298K, pH 7.3
|
Resolution 1.73 Å R-free 0.233 |
| 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–510（147 aa）
Fragment：THROMBIN HEAVY CHAIN
Chain H
518–622（105 aa）
Fragment：THROMBIN HEAVY CHAIN
Chain L
333–361（29 aa）
Fragment：THROMBIN LIGHT CHAIN
|
Not recorded | 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–511（148 aa）
Fragment：THROMBIN HEAVY CHAIN
Chain H
518–622（105 aa）
Fragment：THROMBIN HEAVY CHAIN
Chain L
334–360（27 aa）
Fragment：THROMBIN LIGHT CHAIN
|
Not recorded | 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 |
| 1HAG THE ISOMORPHOUS STRUCTURES OF PRETHROMBIN2, HIRUGEN-AND PPACK-THROMBIN: CHANGES ACCOMPANYING ACTIVATION AND EXOSITE BINDING TO THROMBIN Deposited 1994-06-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
328–622（295 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.00 Å |
| 1HAH THE ISOMORPHOUS STRUCTURES OF PRETHROMBIN2, HIRUGEN-AND PPACK-THROMBIN: CHANGES ACCOMPANYING ACTIVATION AND EXOSITE BINDING TO THROMBIN Deposited 1994-06-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å |
| 1HAI THE ISOMORPHOUS STRUCTURES OF PRETHROMBIN2, HIRUGEN-AND PPACK-THROMBIN: CHANGES ACCOMPANYING ACTIVATION AND EXOSITE BINDING TO THROMBIN Deposited 1994-06-27 | Different construct Different mutation/modification 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
364–622（259 aa）
Chain L
328–363（36 aa）
|
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 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.40 Å |
| 1HAO COMPLEX OF HUMAN ALPHA-THROMBIN WITH A 15MER OLIGONUCLEOTIDE GGTTGGTGTGGTTGG (BASED ON NMR MODEL OF DNA) Deposited 1995-10-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：RESIDUES 364-622
Chain L
328–363（36 aa）
Fragment：RESIDUES 328-363
|
Not recorded | 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.80 Å |
| 1HAP COMPLEX OF HUMAN ALPHA-THROMBIN WITH A 15MER OLIGONUCLEOTIDE GGTTGGTGTGGTTGG (BASED ON X-RAY MODEL OF DNA) Deposited 1995-10-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：residues 364-622
Chain L
328–363（36 aa）
Fragment：residues 328-363
|
Not recorded | 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.80 Å |
| 1HBT Human alpha-thrombin complexed with a peptidyl pyridinium methyl ketone containing bivalent inhibitor Deposited 1995-04-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.00 Å |
| 1HDT STRUCTURE OF A RETRO-BINDING PEPTIDE INHIBITOR COMPLEXED WITH HUMAN ALPHA-THROMBIN Deposited 1994-07-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
331–363（33 aa）
|
Not recorded | 0E7 methyl N-(4-carbamimidamidobutanoyl)-L-phenylalanyl-L-allothreonyl-L-phenylalaninate × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.60 Å |
| 1HGT STRUCTURE OF THE HIRUGEN AND HIRULOG 1 COMPLEXES OF ALPHA-THROMBIN Deposited 1991-06-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.20 Å |
| 1HLT THE STRUCTURE OF A NONADECAPEPTIDE OF THE FIFTH EGF DOMAIN OF THROMBOMODULIN COMPLEXED WITH THROMBIN Deposited 1994-08-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain H
364–622（259 aa）
Chain J
334–360（27 aa）
Chain K
364–622（259 aa）
Chain L
334–360（27 aa）
|
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 mmCIF provides none of the parsed conditions | Resolution 3.00 Å |
| 1HUT THE STRUCTURE OF ALPHA-THROMBIN INHIBITED BY A 15-MER SINGLE-STRANDED DNA APTAMER Deposited 1993-05-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：RESIDUES 364-622
Chain L
328–363（36 aa）
Fragment：RESIDUES 328-363
|
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 2.90 Å |
| 1HXE SERINE PROTEASE Deposited 1995-12-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.10 Å |
| 1IHS CRYSTAL STRUCTURE OF THE COMPLEX OF HUMAN ALPHA-THROMBIN AND NON-HYDROLYZABLE BIFUNCTIONAL INHIBITORS, HIRUTONIN-2 AND HIRUTONIN-6 Deposited 1993-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.00 Å |
| 1IHT CRYSTAL STRUCTURE OF THE COMPLEX OF HUMAN ALPHA-THROMBIN AND NON-HYDROLYZABLE BIFUNCTIONAL INHIBITORS, HIRUTONIN-2 AND HIRUTONIN-6 Deposited 1993-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.10 Å |
| 1JMO Crystal Structure of the Heparin Cofactor II-S195A Thrombin Complex Deposited 2001-07-19 | Different construct 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 H
363–622（260 aa）
Fragment：heavy chain
Chain L
315–362（48 aa）
Fragment：light chain
|
Mutation：S195A | NA SODIUM ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；NH4Cl, PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 298K
|
Resolution 2.20 Å R-free 0.211 |
| 1JOU Crystal Structure of Native S195A Thrombin with an Unoccupied Active Site Deposited 2001-07-31 | Different construct Different mutation/modification 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
315–363（49 aa）
Fragment：Factor Xa cleavage product light chain
Chain B
364–622（259 aa）
Fragment：Factor Xa cleavage product heavy chain
|
Mutation：S195A | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 GOL GLYCEROL × 4 ACY ACETIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；ammonium acetate, sodium citrate, PEG 4000, glycerol, pH 5.6, VAPOR DIFFUSION,
HANGING DROP at 298K, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 1.80 Å R-free 0.245 |
| 1JOU Crystal Structure of Native S195A Thrombin with an Unoccupied Active Site Deposited 2001-07-31 | Different construct Different mutation/modification 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
315–363（49 aa）
Fragment：Factor Xa cleavage product light chain
Chain D
364–622（259 aa）
Fragment：Factor Xa cleavage product heavy chain
|
Mutation：S195A | NA SODIUM ION × 1 ACY ACETIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；ammonium acetate, sodium citrate, PEG 4000, glycerol, pH 5.6, VAPOR DIFFUSION,
HANGING DROP at 298K, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 1.80 Å R-free 0.245 |
| 1JOU Crystal Structure of Native S195A Thrombin with an Unoccupied Active Site Deposited 2001-07-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain E
315–363（49 aa）
Fragment：Factor Xa cleavage product light chain
Chain F
364–622（259 aa）
Fragment：Factor Xa cleavage product heavy chain
|
Mutation：S195A | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 ACY ACETIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；ammonium acetate, sodium citrate, PEG 4000, glycerol, pH 5.6, VAPOR DIFFUSION,
HANGING DROP at 298K, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 1.80 Å R-free 0.245 |
| 1JWT CRYSTAL STRUCTURE OF THROMBIN IN COMPLEX WITH A NOVEL BICYCLIC LACTAM INHIBITOR Deposited 2001-09-05 | Different construct 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
328–622（295 aa）
Fragment：Residues 328-622
|
Not recorded | BLI 4-OXO-2-PHENYLMETHANESULFONYL-OCTAHYDRO-PYRROLO[1,2-A]PYRAZINE-6-CARBOXYLIC ACID [1-(N-HYDROXYCARBAMIMIDOYL)-PIPERIDIN-4-YLMETHYL]-AMIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.50 Å R-free 0.301 |
| 1K21 HUMAN THROMBIN-INHIBITOR COMPLEX Deposited 2001-09-26 | Different construct 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 H
364–622（259 aa）
Fragment：THROMBIN HEAVY CHAIN, Residues 364-622
Chain L
328–363（36 aa）
Fragment：THROMBIN LIGHT CHAIN, Residues 323-363
|
Not recorded | NA SODIUM ION × 2 IGN {[(1R)-2-((2S)-2-{[(3-{[AMINO(IMINO)METHYL]AMINO}PROPYL)AMINO]CARBONYL}PIPERIDINYL)-1-(CYCLOHEXYLMETHYL)-2-OXOETHYL]AMINO}ACETIC ACID × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.86 Å R-free 0.256 |
| 1K22 HUMAN THROMBIN-INHIBITOR COMPLEX Deposited 2001-09-26 | Different construct 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 H
364–622（259 aa）
Fragment：THROMBIN HEAVY CHAIN, Residues 364-622
Chain L
328–363（36 aa）
Fragment：THROMBIN LIGHT CHAIN, Residues 323-363
|
Not recorded | NA SODIUM ION × 2 MEL [((1R)-2-{(2S)-2-[({4-[AMINO(IMINO)METHYL]BENZYL}AMINO)CARBONYL]AZETIDINYL}-1-CYCLOHEXYL-2-OXOETHYL)AMINO]ACETIC ACID × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.93 Å R-free 0.214 |
| 1KTS Thrombin Inhibitor Complex Deposited 2002-01-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：light chain
Chain B
364–622（259 aa）
Fragment：heavy chain
|
Not recorded | C24 3-({2-[(4-CARBAMIMIDOYL-PHENYLAMINO)-METHYL]-3-METHYL-3H-BENZOIMIDAZOLE-5-CARBONYL}-PYRIDIN-2-YL-AMINO)-PROPIONIC ACID ETHYL ESTER × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.40 Å R-free 0.309 |
| 1KTT Thrombin inhibitor complex Deposited 2002-01-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：light chain
Chain B
364–622（259 aa）
Fragment：heavy chain
|
Not recorded | C02 4-(5-BENZENESULFONYLAMINO-1-METHYL-1H-BENZOIMIDAZOL-2-YLMETHYL)-BENZAMIDINE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.10 Å R-free 0.259 |
| 1LHC HUMAN ALPHA-THROMBIN COMPLEXED WITH AC-(D)PHE-PRO-BOROARG-OH Deposited 1994-12-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | DP7 AC-(D)PHE-PRO-BOROARG-OH × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.95 Å |
| 1LHD HUMAN ALPHA-THROMBIN COMPLEXED WITH AC-(D)PHE-PRO-BOROLYS-OH Deposited 1994-12-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | DI2 AC-(D)PHE-PRO-BOROLYS-OH × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.35 Å |
| 1LHE HUMAN ALPHA-THROMBIN COMPLEXED WITH AC-(D)PHE-PRO-BORO-N-BUTYL-AMIDINO-GLYCINE-OH Deposited 1994-12-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | DI3 AC-(D)PHE-PRO-BORO-N-BUTYL-AMIDINO-GLYCINE-OH × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.25 Å |
| 1LHF HUMAN ALPHA-THROMBIN COMPLEXED WITH AC-(D)PHE-PRO-BORO-HOMOLYS-OH Deposited 1994-12-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | DI4 AC-(D)PHE-PRO-BOROHOMOLYS-OH × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.40 Å |
| 1LHG HUMAN ALPHA-THROMBIN COMPLEXED WITH AC-(D)PHE-PRO-BOROORNITHINE-OH Deposited 1994-12-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | DI5 AC-(D)PHE-PRO-BOROHOMOORNITHINE-OH × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.25 Å |
| 1MH0 Crystal structure of the anticoagulant slow form of thrombin Deposited 2002-08-18 | 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
334–620（287 aa）
|
Mutation：R77aA | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；PEG 2000-Monomethyl ether, Tris-Cl, pH 7.6, VAPOR DIFFUSION, HANGING DROP at 298K
|
Resolution 2.80 Å R-free 0.275 |
| 1MH0 Crystal structure of the anticoagulant slow form of thrombin Deposited 2002-08-18 | 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 B
334–620（287 aa）
|
Mutation：R77aA | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；PEG 2000-Monomethyl ether, Tris-Cl, pH 7.6, VAPOR DIFFUSION, HANGING DROP at 298K
|
Resolution 2.80 Å R-free 0.275 |
| 1MU6 Crystal Structure of Thrombin in Complex with L-378,622 Deposited 2002-09-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：light chain
Chain B
364–622（259 aa）
Fragment：heavy chain
|
Not recorded | CDA 2-(6-CHLORO-3-{[2,2-DIFLUORO-2-(2-PYRIDINYL)ETHYL]AMINO}-2-OXO-1(2H)-PYRAZINYL)-N-[(2-FLUORO-6-PYRIDINYL)METHYL]ACETAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；295 K；pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.99 Å R-free 0.235 |
| 1MU8 thrombin-hirugen_l-378,650 Deposited 2002-09-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：light chain
Chain B
364–622（259 aa）
Fragment：heavy chain
|
Not recorded | CDB 2-(6-CHLORO-3-{[2,2-DIFLUORO-2-(2-PYRIDINYL)ETHYL]AMINO}-2-OXO-1(2H)-PYRAZINYL)-N-[(2-FLUORO-3-METHYL-6-PYRIDINYL)METHYL]ACETAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；295 K；pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.00 Å |
| 1MUE Thrombin-Hirugen-L405,426 Deposited 2002-09-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：light chain
Chain B
364–622（259 aa）
Fragment：heavy chain
|
Not recorded | CDD 2-(6-CHLORO-3-{[2,2-DIFLUORO-2-(1-OXIDO-2-PYRIDINYL)ETHYL]AMINO}-2-OXO-1(2H)-PYRAZINYL)-N-[(2-FLUOROPHENYL)METHYL]ACETAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.00 Å |
| 1NM6 thrombin in complex with selective macrocyclic inhibitor at 1.8A Deposited 2003-01-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
335–621（287 aa）
|
Not recorded | L86 (11S)-11-BENZYL-6-CHLORO-1,2,10,11,12,13,14,15,16,17,18,19-DODECAHYDRO-5,9-METHANO-2,5,8,10,13,17-BENZOHEXAAZACYCLOHENI COSINE-3,24-DIONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 8000, sodium phosphate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.80 Å R-free 0.238 |
| 1NO9 Design of weakly basic thrombin inhibitors incorporating novel P1 binding functions: molecular and X-ray crystallographic studies. Deposited 2003-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：Heavy Chain
Chain L
328–363（36 aa）
Fragment：Light Chain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 4ND N4-(N,N-DIPHENYLCARBAMOYL)-AMINOGUANIDINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 4000, Sodium Chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.204 |
| 1NRN CRYSTALLOGRAPHIC STRUCTURES OF THROMBIN COMPLEXED WITH THROMBIN RECEPTOR PEPTIDES: EXISTENCE OF EXPECTED AND NOVEL BINDING MODES Deposited 1994-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.10 Å |
| 1NRO CRYSTALLOGRAPHIC STRUCTURES OF THROMBIN COMPLEXED WITH THROMBIN RECEPTOR PEPTIDES: EXISTENCE OF EXPECTED AND NOVEL BINDING MODES Deposited 1994-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.10 Å |
| 1NRP CRYSTALLOGRAPHIC STRUCTURES OF THROMBIN COMPLEXED WITH THROMBIN RECEPTOR PEPTIDES: EXISTENCE OF EXPECTED AND NOVEL BINDING MODES Deposited 1994-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.00 Å |
| 1NRQ CRYSTALLOGRAPHIC STRUCTURES OF THROMBIN COMPLEXED WITH THROMBIN RECEPTOR PEPTIDES: EXISTENCE OF EXPECTED AND NOVEL BINDING MODES Deposited 1994-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.50 Å |
| 1NRR Crystallographic structures of Thrombin complexed with Thrombin receptor peptides: Existence of expected and novel binding modes Deposited 1994-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：RESIDUES 364-622
Chain L
328–363（36 aa）
Fragment：RESIDUES 328-363
|
Not recorded | 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.40 Å |
| 1NRS CRYSTALLOGRAPHIC STRUCTURES OF THROMBIN COMPLEXED WITH THROMBIN RECEPTOR PEPTIDES: EXISTENCE OF EXPECTED AND NOVEL BINDING MODES Deposited 1994-01-18 | 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 H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.40 Å |
| 1NT1 thrombin in complex with selective macrocyclic inhibitor Deposited 2003-01-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
335–621（287 aa）
|
Not recorded | T76 (6R,21AS)-17-CHLORO-6-CYCLOHEXYL-2,3,6,7,10,11,19,20-OCTAHYDRO-1H,5H-PYRROLO[1,2-K][1,4,8,11,14]BENZOXATETRAAZA-CYCLOHEPTADECINE-5,8,12,21(9H,13H,21AH)-TETRONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 8000, sodium phosphate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å |
| 1NU7 Staphylocoagulase-Thrombin Complex Deposited 2003-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
332–359（28 aa）
Fragment：UNP residues 332-359
Chain B
364–622（259 aa）
Fragment：UNP residues 364-622
|
Not recorded | 0ZJ N-(sulfanylacetyl)-D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 HG MERCURY (II) ION × 2 IMD IMIDAZOLE × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；100mM imidazole, 200mM sodium formate, 12%(w/v) PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.20 Å R-free 0.249 |
| 1NU7 Staphylocoagulase-Thrombin Complex Deposited 2003-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
332–359（28 aa）
Fragment：UNP residues 332-359
Chain F
364–622（259 aa）
Fragment：UNP residues 364-622
|
Not recorded | 0ZJ N-(sulfanylacetyl)-D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 HG MERCURY (II) ION × 2 IMD IMIDAZOLE × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；100mM imidazole, 200mM sodium formate, 12%(w/v) PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.20 Å R-free 0.249 |
| 1NU9 Staphylocoagulase-Prethrombin-2 complex Deposited 2003-01-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
332–622（291 aa）
|
Not recorded | 0ZJ N-(sulfanylacetyl)-D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 HG MERCURY (II) ION × 2 IMD IMIDAZOLE × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；100mM imidazole, 200mM sodium formate, 12%(w/v) PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.20 Å R-free 0.253 |
| 1NU9 Staphylocoagulase-Prethrombin-2 complex Deposited 2003-01-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
332–622（291 aa）
|
Not recorded | 0ZJ N-(sulfanylacetyl)-D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 HG MERCURY (II) ION × 2 IMD IMIDAZOLE × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；100mM imidazole, 200mM sodium formate, 12%(w/v) PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.20 Å R-free 0.253 |
| 1NY2 Human alpha thrombin inhibited by RPPGF and hirugen Deposited 2003-02-11 | 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 1
328–363（36 aa）
Fragment：light chain A
Chain 2
364–622（259 aa）
Fragment：heavy chain B
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；PEG 4000, ammonium sulphate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 25K, temperature 298K
|
Resolution 2.30 Å |
| 1NZQ D-Phe-Pro-Arg-Type Thrombin Inhibitor Deposited 2003-02-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：heavy chain
Chain L
328–363（36 aa）
Fragment：light chain
|
Not recorded | 162 (2-{2-[(5-CARBAMIMIDOYL-1-METHYL-1H-PYRROL-3-YLMETHYL)-CARBAMOYL]-PYRROL-1-YL} -1-CYCLOHEXYLMETHYL-2-OXO-ETHYLAMINO)-ACETIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；PEG 400, Na-acetate, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
|
Resolution 2.18 Å R-free 0.242 |
| 1O0D Human Thrombin complexed with a d-Phe-Pro-Arg-type Inhibitor and a C-terminal Hirudin derived exo-site inhibitor Deposited 2003-02-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：heavy chain
Chain L
328–363（36 aa）
Fragment：light chain
|
Not recorded | 163 (2-{2-[(5-CARBAMIMIDOYL-1-METHYL-1H-PYRROL-2-YLMETHYL)-CARBAMOYL]-PYRROL-1-YL}- 1-CYCLOHEXYLMETHYL-2-OXO-ETHYLAMINO)-ACETIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；PEG 400, Na-acetate, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
|
Resolution 2.44 Å R-free 0.252 |
| 1O0D Human Thrombin complexed with a d-Phe-Pro-Arg-type Inhibitor and a C-terminal Hirudin derived exo-site inhibitor Deposited 2003-02-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain H
364–622（259 aa）
Fragment：heavy chain
Chain L
328–363（36 aa）
Fragment：light chain
|
Not recorded | 163 (2-{2-[(5-CARBAMIMIDOYL-1-METHYL-1H-PYRROL-2-YLMETHYL)-CARBAMOYL]-PYRROL-1-YL}- 1-CYCLOHEXYLMETHYL-2-OXO-ETHYLAMINO)-ACETIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；PEG 400, Na-acetate, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
|
Resolution 2.44 Å R-free 0.252 |
| 1O2G Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors Deposited 2003-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：HEAVY CHAIN, RESIDUES 364-620
Chain L
328–363（36 aa）
Fragment：LIGHT CHAIN, RESIDUES 328-363
|
Not recorded | NA SODIUM ION × 1 696 3-{5-[AMINO(IMINIO)METHYL]-1H-INDOL-2-YL}-1,1'-BIPHENYL-2-OLATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；298 K；2-propanol, PEG 4000, pH 6.5, vapor diffusion at 298 K, pH 6.50
|
Resolution 1.58 Å R-free 0.250 |
| 1O5G Dissecting and Designing Inhibitor Selectivity Determinants at the S1 site Using an Artificial Ala190 Protease (Ala190 uPA) Deposited 2003-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：HEAVY CHAIN, RESIDUES 364-620
Chain L
328–363（36 aa）
Fragment：LIGHT CHAIN, RESIDUES 328-363
|
Not recorded | NA SODIUM ION × 1 CA CALCIUM ION × 1 CR9 2-{5-[AMINO(IMINIO)METHYL]-6-FLUORO-1H-BENZIMIDAZOL-2-YL}-6-[(2-METHYLCYCLOHEXYL)OXY]BENZENOLATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；298 K；2-propanol, PEG 4000, pH 6.5, vapor diffusion at 298 K, pH 7.50
|
Resolution 1.75 Å R-free 0.238 |
| 1OOK Crystal Structure of the Complex of Platelet Receptor GPIb-alpha and Human alpha-Thrombin Deposited 2003-03-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
328–363（36 aa）
Fragment：THROMBIN A CHAIN
Chain B
364–622（259 aa）
Fragment：THROMBIN B CHAIN
|
Not recorded | CL CHLORIDE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 6000, Ammonium Phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
|
Resolution 2.30 Å R-free 0.260 |
| 1OYT COMPLEX OF RECOMBINANT HUMAN THROMBIN WITH A DESIGNED FLUORINATED INHIBITOR Deposited 2003-04-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 1 CA CALCIUM ION × 1 FSN (3ASR,4RS,8ASR,8BRS)-4-(2-(4-FLUOROBENZYL)-1,3-DIOXODEACAHYDROPYRROLO[3,4-A] PYRROLIZIN-4-YL)BENZAMIDINE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.67 Å R-free 0.205 |
| 1P8V CRYSTAL STRUCTURE OF THE COMPLEX OF PLATELET RECEPTOR GPIB-ALPHA AND ALPHA-THROMBIN AT 2.6A Deposited 2003-05-07 | 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 B
333–361（29 aa）
Fragment：Alpha Thrombin, light chain
Chain C
364–621（258 aa）
Fragment：Alpha Thrombin, heavy chain
|
Not recorded | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 DFP DIISOPROPYL PHOSPHONATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；291 K；14% PEG 400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 6.00
|
Resolution 2.60 Å R-free 0.238 |
| 1PPB THE REFINED 1.9 ANGSTROMS CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN: INTERACTION WITH D-PHE-PRO-ARG CHLOROMETHYLKETONE AND SIGNIFICANCE OF THE TYR-PRO-PRO-TRP INSERTION SEGMENT Deposited 1991-10-24 | Different construct Different mutation/modification 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
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.92 Å |
| 1QBV CRYSTAL STRUCTURE OF THROMBIN COMPLEXED WITH AN GUANIDINE-MIMETIC INHIBITOR Deposited 1999-04-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：HEAVY CHAIN
Chain L
328–363（36 aa）
Fragment：LIGHT CHAIN
|
Not recorded | PPX [PHENYLALANINYL-PROLINYL]-[2-(PYRIDIN-4-YLAMINO)-ETHYL]-AMINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；277.15 K；PEG 8000, phosphate, NaCl, NAN3, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.80 Å |
| 1QHR NOVEL COVALENT ACTIVE SITE THROMBIN INHIBITORS Deposited 1999-05-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–36（36 aa）
Fragment：LIGHT CHAIN
Chain B
364–622（259 aa）
Fragment：HEAVY CHAIN
|
Not recorded | 157 6-(2-HYDROXY-CYCLOPENTYL)-7-OXO-HEPTANAMIDINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；CRYSTALS WERE GROWN BY MACROSEEDING A SOLUTION OF 100MM HEPES PH 7.0, 22% PEG4K, 200MM NACL. PROTEIN CONCENTRATION OF 5MG/ML.
|
Resolution 2.20 Å |
| 1QJ1 Novel Covalent Active Site Thrombin Inhibitors Deposited 1999-06-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：ALPHA THROMBIN LIGHT CHAIN
Chain B
364–622（259 aa）
Fragment：ALPHA THROMBIN HEAVY CHAIN
|
Not recorded | 166 6-CARBAMIMIDOYL-2-[2-HYDROXY-6-(4-HYDROXY-PHENYL)-INDAN-1-YL]-HEXANOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；CRYSTALS WERE GROWN BY MACROSEEDING A SOLUTION OF 100MM HEPES PH 7.0, 22% PEG4K, 200MM NACL. PROTEIN CONCENTRATION OF 5MG/ML.
|
Resolution 2.00 Å |
| 1QJ6 Novel Covalent Active Site Thrombin Inhibitors Deposited 1999-06-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：ALPHA THROMBIN, RESIDUES 328-363
Chain B
364–622（259 aa）
Fragment：ALPHA THROMBIN, RESIDUES 364-622
|
Not recorded | 167 6-CARBAMIMIDOYL-2-[2-HYDROXY-5-(3-METHOXY-PHENYL)-INDAN-1-YL]-HEXANOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；CRYSTALS WERE GROWN BY MACROSEEDING A SOLUTION OF 100MM HEPES PH 7.0, 22% PEG4K, 200MM NACL. PROTEIN CONCENTRATION OF 5MG/ML.
|
Resolution 2.20 Å |
| 1QJ7 Novel Covalent Active Site Thrombin Inhibitors Deposited 1999-06-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：ALPHA THROMBIN, RESIDUES 328-363
Chain B
364–622（259 aa）
Fragment：ALPHA THROMBIN, RESIDUES 364-622
|
Not recorded | GR1 6-CARBAMIMIDOYL-2-[5-(3-DIETHYLCARBAMOYL-PHENYL)-2-HYDROXY-INDAN-1-YL]-HEXANOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；CRYSTALS WERE GROWN BY MACROSEEDING A SOLUTION OF 100MM HEPES PH 7.0, 22% PEG4K, 200MM NACL. PROTEIN CONCENTRATION OF 5MG/ML.
|
Resolution 2.20 Å |
| 1QUR HUMAN ALPHA-THROMBIN IN COMPLEX WITH BIVALENT, BENZAMIDINE-BASED SYNTHETIC INHIBITOR Deposited 1999-07-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Chain L
334–360（27 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
macro seeding；280 K；100 mM Tris/HCl, 300-500 mM NaCl, 22-32% (w/v) PEG 8000, macro seeding, temperature 280K
|
Resolution 2.00 Å R-free 0.246 |
| 1RD3 2.5A Structure of Anticoagulant Thrombin Variant E217K Deposited 2003-11-05 | 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
328–363（36 aa）
Fragment：Thrombin light chain
Chain B
364–622（259 aa）
Fragment：Thrombin heavy chain
Chain C
328–363（36 aa）
Fragment：Thrombin light chain
Chain D
364–622（259 aa）
Fragment：Thrombin heavy chain
|
Mutation：E217K Mutation：E217K | PO4 PHOSPHATE ION × 3 GOL GLYCEROL × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；sodium tris, potassium phosphate, glycerol, PEG 8000, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.50 Å R-free 0.259 |
| 1RD3 2.5A Structure of Anticoagulant Thrombin Variant E217K Deposited 2003-11-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
328–363（36 aa）
Fragment：Thrombin light chain
Chain B
364–622（259 aa）
Fragment：Thrombin heavy chain
|
Mutation：E217K | PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；sodium tris, potassium phosphate, glycerol, PEG 8000, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.50 Å R-free 0.259 |
| 1RD3 2.5A Structure of Anticoagulant Thrombin Variant E217K Deposited 2003-11-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
328–363（36 aa）
Fragment：Thrombin light chain
Chain D
364–622（259 aa）
Fragment：Thrombin heavy chain
|
Mutation：E217K | PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；sodium tris, potassium phosphate, glycerol, PEG 8000, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.50 Å R-free 0.259 |
| 1RIW Thrombin in complex with natural product inhibitor Oscillarin Deposited 2003-11-18 | 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 A
328–363（36 aa）
Chain B
364–510（147 aa）
Fragment：residues 37-183
Chain C
518–622（105 aa）
Fragment：residues 185-286
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 OSC (2R,3AS,6R,7AS)-N-(2-{1-[AMINO(IMINO)METHYL]-2,5-DIHYDRO-1H-PYRROL-3-YL}ETHYL)-6-HYDROXY-1-{N-[(2S)-2-HYDROXY-3-PHENYLPROPANOYL]PHENYLALANYL}OCTAHYDRO-1H-INDOLE-2-CARBOXAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；PEG 8000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.04 Å R-free 0.232 |
| 1SB1 Novel Non-Covalent Thrombin Inhibitors Incorporating P1 4,5,6,7-Tetrahydrobenzothiazole Arginine Side Chain Mimetics Deposited 2004-02-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Fragment：heavy chain, residues 364-621
Chain L
333–361（29 aa）
Fragment：light chain, residues 333-361
|
Not recorded | NA SODIUM ION × 2 165 N-(BENZYLSULFONYL)-3-CYCLOHEXYLALANYL-N-(2-AMINO-1,3-BENZOTHIAZOL-6-YL)PROLINAMIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.90 Å R-free 0.224 |
| 1SFQ Fast form of thrombin mutant R(77a)A bound to PPACK Deposited 2004-02-20 | Different construct Different mutation/modification 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
328–363（36 aa）
Fragment：thrombin light chain (A)
Chain B
364–622（259 aa）
Fragment：thrombin heavy chain (B)
|
Mutation：R(77a)A | 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, HANGING DROP；pH 6.6；293 K；PEG monomethyl ether 2000, Bis-Tris, sodium chloride, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.91 Å R-free 0.221 |
| 1SFQ Fast form of thrombin mutant R(77a)A bound to PPACK Deposited 2004-02-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain D
328–363（36 aa）
Fragment：thrombin light chain (A)
Chain E
364–622（259 aa）
Fragment：thrombin heavy chain (B)
|
Mutation：R(77a)A | 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, HANGING DROP；pH 6.6；293 K；PEG monomethyl ether 2000, Bis-Tris, sodium chloride, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.91 Å R-free 0.221 |
| 1SG8 Crystal structure of the procoagulant fast form of thrombin Deposited 2004-02-23 | Different construct Different mutation/modification 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
328–363（36 aa）
Fragment：thrombin light chain (A)
Chain B
364–622（259 aa）
Fragment：thrombin heavy chain (B)
|
Mutation：R(77a)A | 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 7.5；298 K；19% PEG 2000-MME, 0.1 M Bis-Tris, 200 mM NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.30 Å R-free 0.289 |
| 1SG8 Crystal structure of the procoagulant fast form of thrombin Deposited 2004-02-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain D
328–363（36 aa）
Fragment：thrombin light chain (A)
Chain E
364–622（259 aa）
Fragment：thrombin heavy chain (B)
|
Mutation：R(77a)A | 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 7.5；298 K；19% PEG 2000-MME, 0.1 M Bis-Tris, 200 mM NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.30 Å R-free 0.289 |
| 1SG8 Crystal structure of the procoagulant fast form of thrombin Deposited 2004-02-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
328–363（36 aa）
Fragment：thrombin light chain (A)
Chain B
364–622（259 aa）
Fragment：thrombin heavy chain (B)
Chain D
328–363（36 aa）
Fragment：thrombin light chain (A)
Chain E
364–622（259 aa）
Fragment：thrombin heavy chain (B)
|
Mutation：R(77a)A Mutation：R(77a)A | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；19% PEG 2000-MME, 0.1 M Bis-Tris, 200 mM NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.30 Å R-free 0.289 |
| 1SGI Crystal structure of the anticoagulant slow form of thrombin Deposited 2004-02-23 | Different construct Different mutation/modification 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
328–363（36 aa）
Fragment：THROMBIN LIGHT CHAIN (A)
Chain B
364–622（259 aa）
Fragment：THROMBIN HEAVY CHAIN (B)
|
Mutation：R(77a)A | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；14% PEG 2000-MME, 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.30 Å R-free 0.251 |
| 1SGI Crystal structure of the anticoagulant slow form of thrombin Deposited 2004-02-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain D
328–363（36 aa）
Fragment：THROMBIN LIGHT CHAIN (A)
Chain E
364–622（259 aa）
Fragment：THROMBIN HEAVY CHAIN (B)
|
Mutation：R(77a)A | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；14% PEG 2000-MME, 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.30 Å R-free 0.251 |
| 1SHH Slow form of Thrombin Bound with PPACK Deposited 2004-02-25 | Different construct Different mutation/modification 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
328–363（36 aa）
Fragment：THROMBIN LIGHT CHAIN (A)
Chain B
364–622（259 aa）
Fragment：THROMBIN HEAVY CHAIN (B)
|
Mutation：R77aA | 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；16-22% PEG monomethyl ether 2000, 50 mM Bis-tris, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 1.55 Å R-free 0.216 |
| 1SHH Slow form of Thrombin Bound with PPACK Deposited 2004-02-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain D
328–363（36 aa）
Fragment：THROMBIN LIGHT CHAIN (A)
Chain E
364–622（259 aa）
Fragment：THROMBIN HEAVY CHAIN (B)
|
Mutation：R77aA | 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 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；16-22% PEG monomethyl ether 2000, 50 mM Bis-tris, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 1.55 Å R-free 0.216 |
| 1SL3 crystal structue of Thrombin in complex with a potent P1 heterocycle-Aryl based inhibitor Deposited 2004-03-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
335–621（287 aa）
Fragment：alpha-thrombin
|
Not recorded | 170 (2-[6-CHLORO-3-{[2,2-DIFLUORO-2-(1-OXIDOPYRIDIN-2-YL)ETHYL]AMINO}-2-OXOPYRAZIN-1(2H)-YL]-N-[5-CHLORO-2-(1H-TETRAZOL-1-YL)BENZYL]ACETAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 8000, sodium phosphate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.81 Å R-free 0.240 |
| 1SR5 ANTITHROMBIN-ANHYDROTHROMBIN-HEPARIN TERNARY COMPLEX STRUCTURE Deposited 2004-03-22 | Different construct 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 B
328–363（36 aa）
Fragment：light chain (residues 328-363)
Chain C
364–622（259 aa）
Fragment：heavy chain (residues 364-622)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GU4 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.4；291 K；PEG 3350, tri-sodium citrate, pH 8.40, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
|
Resolution 3.10 Å R-free 0.278 |
| 1T4U Crystal Structure Analysis of a novel Oxyguanidine bound to Thrombin Deposited 2004-04-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：sequence database residues 364-622
Chain L
334–359（26 aa）
Fragment：sequence database residues 334-359
|
Not recorded | 81A 2-METHANESULFONYL-BENZENESULFONIC ACID 3-METHYL-5-((1-AMIDINOAMINOOXYMETHYL-CYCLOPROPYL)METHYLOXY)-PHENYLESTER × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.00 Å |
| 1T4V Crystal Structure Analysis of a novel Oxyguanidine bound to Thrombin Deposited 2004-04-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：sequence database residues 364-622
Chain L
334–359（26 aa）
Fragment：sequence database residues 334-359
|
Not recorded | 14A N-ALLYL-5-AMIDINOAMINOOXY-PROPYLOXY-3-CHLORO-N-CYCLOPENTYLBENZAMIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.00 Å |
| 1TA2 Crystal structure of thrombin in complex with compound 1 Deposited 2004-05-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
335–621（287 aa）
Fragment：alpha-thrombin
|
Not recorded | 176 1-(2-AMINO-3,3-DIPHENYL-PROPIONYL)-PYRROLIDINE-3-CARBOXYLIC ACID 2,5-DICHLORO-BENZYLAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 8000, Sodium phosphate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.30 Å |
| 1TA6 Crystal structure of thrombin in complex with compound 14b Deposited 2004-05-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
335–621（287 aa）
Fragment：alpha-thrombin
|
Not recorded | 177 1-[2-AMINO-2-CYCLOHEXYL-ACETYL]-PYRROLIDINE-3-CARBOXYLIC ACID 5-CHLORO-2-(2-ETHYLCARBAMOYL-ETHOXY)-BENZYLAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 8000, Sodium phosphate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.90 Å |
| 1TB6 2.5A Crystal Structure of the Antithrombin-Thrombin-Heparin Ternary Complex Deposited 2004-05-19 | Different construct 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 H
364–622（259 aa）
Fragment：thrombin heavy chain, serine protease
Chain L
315–363（49 aa）
Fragment：thrombin light chain
|
Mutation：S195A | MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；296 K；PEG 3350, lithium citrate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K
|
Resolution 2.50 Å R-free 0.245 |
| 1TBZ HUMAN THROMBIN WITH ACTIVE SITE N-METHYL-D PHENYLALANYL-N-[5-(AMINOIMINOMETHYL)AMINO]-1-{{BENZOTHIAZOLYL)CARBONYL] BUTYL]-L-PROLINAMIDE TRIFLUROACETATE AND EXOSITE-HIRUGEN Deposited 1998-02-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 00Q D-phenylalanyl-N-{(1S)-1-[(S)-1,3-benzothiazol-2-yl(hydroxy)methyl]-4-carbamimidamidobutyl}-L-prolinamide × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion - hanging drop - macroseeding；pH 7.3；0.1M PHOSPHATE BUFFER AT PH 7.3, 27-28% PEG 8000. HANGING DROPS AND MACROSEEDING ., vapor diffusion - hanging drop - macroseeding
|
Resolution 2.30 Å |
| 1THP STRUCTURE OF HUMAN ALPHA-THROMBIN Y225P MUTANT BOUND TO D-PHE-PRO-ARG-CHLOROMETHYLKETONE Deposited 1999-01-26 | Different construct Different mutation/modification 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
328–363（36 aa）
Chain B
364–622（259 aa）
|
Mutation：Y225P | 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；pH 7.5
|
Resolution 2.10 Å R-free 0.272 |
| 1THR STRUCTURES OF THROMBIN COMPLEXES WITH A DESIGNED AND A NATURAL EXOSITE INHIBITOR Deposited 1993-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å |
| 1THS STRUCTURES OF THROMBIN COMPLEXES WITH A DESIGNED AND A NATURAL EXOSITE INHIBITOR Deposited 1993-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.20 Å |
| 1THS STRUCTURES OF THROMBIN COMPLEXES WITH A DESIGNED AND A NATURAL EXOSITE INHIBITOR Deposited 1993-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.20 Å |
| 1TMB MOLECULAR BASIS FOR THE INHIBITION OF HUMAN ALPHA-THROMBIN BY THE MACROCYCLIC PEPTIDE CYCLOTHEONAMIDE A Deposited 1993-05-27 | 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 H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å |
| 1TMT CHANGES IN INTERACTIONS IN COMPLEXES OF HIRUDIN DERIVATIVES AND HUMAN ALPHA-THROMBIN DUE TO DIFFERENT CRYSTAL FORMS Deposited 1994-05-26 | 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 H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.20 Å |
| 1TMU Changes in interactions in complexes of hirudin derivatives and human alpha-thrombin due to different crystal forms Deposited 1994-05-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：residues 364-622
Chain L
333–360（28 aa）
Fragment：residues 328-363
|
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 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.50 Å |
| 1TOM ALPHA-THROMBIN COMPLEXED WITH HIRUGEN Deposited 1996-12-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | MIN METHYL-PHE-PRO-AMINO-CYCLOHEXYLGLYCINE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å |
| 1TQ0 Crystal structure of the potent anticoagulant thrombin mutant W215A/E217A in free form Deposited 2004-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
333–363（31 aa）
Fragment：light chain
Chain B
364–620（257 aa）
Fragment：heavy chain
Chain C
333–363（31 aa）
Fragment：light chain
Chain D
364–620（257 aa）
Fragment：heavy chain
|
Mutation：W215A/E217A Mutation：W215A/E217A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.9；298 K；0.1 M CAPS, 0.2 M lithium sulfate, 0.12 M sodium dihydrogen phosphate, 0.53 M dipotassium hydrogen phosphate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.80 Å R-free 0.292 |
| 1TQ0 Crystal structure of the potent anticoagulant thrombin mutant W215A/E217A in free form Deposited 2004-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
333–363（31 aa）
Fragment：light chain
Chain B
364–620（257 aa）
Fragment：heavy chain
|
Mutation：W215A/E217A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.9；298 K；0.1 M CAPS, 0.2 M lithium sulfate, 0.12 M sodium dihydrogen phosphate, 0.53 M dipotassium hydrogen phosphate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.80 Å R-free 0.292 |
| 1TQ0 Crystal structure of the potent anticoagulant thrombin mutant W215A/E217A in free form Deposited 2004-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
333–363（31 aa）
Fragment：light chain
Chain D
364–620（257 aa）
Fragment：heavy chain
|
Mutation：W215A/E217A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.9；298 K；0.1 M CAPS, 0.2 M lithium sulfate, 0.12 M sodium dihydrogen phosphate, 0.53 M dipotassium hydrogen phosphate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.80 Å R-free 0.292 |
| 1TQ7 Crystal structure of the anticoagulant thrombin mutant W215A/E217A bound to PPACK Deposited 2004-06-16 | Different construct Different mutation/modification 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
320–363（44 aa）
Fragment：light chain
Chain B
364–620（257 aa）
Fragment：heavy chain
|
Mutation：W215A/E217A | ZN ZINC ION × 3 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 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；18% PEG 8000, 0.2 M zinc acetate, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.40 Å R-free 0.243 |
| 1TWX Crystal structure of the thrombin mutant D221A/D222K Deposited 2004-07-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–361（28 aa）
Fragment：light chain
Chain B
364–622（259 aa）
Fragment：heavy chain
|
Mutation：D221A/D222K | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；0.1 M sodium phosphate, 26% PEG 8000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.40 Å R-free 0.268 |
| 1UMA ALPHA-THROMBIN (HIRUGEN) COMPLEXED WITH NA-(N,N-DIMETHYLCARBAMOYL)-ALPHA-AZALYSINE Deposited 1996-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 IN2 N,N-DIMETHYLCARBAMOYL-ALPHA-AZALYSINE × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.00 Å |
| 1UVS BOVINE THROMBIN--BM51.1011 COMPLEX Deposited 1996-10-16 | Different construct Different mutation/modification 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
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | I11 [[CYCLOHEXANESULFONYL-GLYCYL]-3[PYRIDIN-4-YL-AMINOMETHYL]ALANYL]PIPERIDINE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.80 Å R-free 0.280 |
| 1VR1 Specifity for Plasminogen Activator Inhibitor-1 Deposited 1998-12-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Chain L
334–360（27 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.6；pH 7.6
|
Resolution 1.90 Å R-free 0.256 |
| 1VZQ Complex of thrombin with designed inhibitor 7165 Deposited 2004-05-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Fragment：SERINE PROTEASE DOMAIN, RESIDUES 364-620
Chain L
334–360（27 aa）
Fragment：RESIDUES 334-360
|
Not recorded | SHY 4-[(3AS,4R,7R,8AS,8BR)-2-(1,3-BENZODIOXOL-5-YLMETHYL)-7-HYDROXY-1,3-DIOXODECAHYDROPYRROLO[3,4-A]PYRROLIZIN-4-YL]BENZENECARBOXIMIDAMIDE × 1 NA SODIUM ION × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.4；PH 7.40
|
Resolution 1.54 Å R-free 0.209 |
| 1W7G Alpha-thrombin complex with sulfated hirudin (residues 54-65) and L- Arginine template inhibitor CS107 Deposited 2004-09-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：THROMBIN HEAVY CHAIN
Chain L
328–363（36 aa）
Fragment：THROMBIN LIGHT CHAIN
|
Not recorded | MIU N-{(1S)-1-{[4-(3-AMINOPROPYL)PIPERAZIN-1-YL]CARBONYL}-4-[(DIAMINOMETHYLENE)AMINO]BUTYL}-3-(TRIFLUOROMETHYL)BENZENESULFONAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；VAPOUR DIFFUSION HANGING DROP 20% P5KMME 0.1M HEPES PH7.5 0.3M NACL THROMBIN 10MG/ML HIRUDIN 3MM AND CS107 16MM, PH 7.50
|
Resolution 1.65 Å R-free 0.272 |
| 1WAY Active site thrombin inhibitors Deposited 2004-10-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：FRAGMENT ALPHA THROMBIN, RESIDUES 328-363
Chain B
364–622（259 aa）
Fragment：FRAGMENT ALPHA THROMBIN, RESIDUES 364-622
|
Not recorded | L02 4-[3-(4-CHLOROPHENYL)-1H-PYRAZOL-5-YL]PIPERIDINE × 1 DMS DIMETHYL SULFOXIDE × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.3；PH 7.30
|
Resolution 2.02 Å R-free 0.231 |
| 1WBG Active site thrombin inhibitors Deposited 2004-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：FRAGMENT ALPHA THROMBIN, RESIDUES 328-363
Chain B
364–622（259 aa）
Fragment：FRAGMENT ALPHA THROMBIN, RESIDUES 364-622
|
Not recorded | L03 3-(4-CHLOROPHENYL)-5-(METHYLTHIO)-4H-1,2,4-TRIAZOLE × 1 DMS DIMETHYL SULFOXIDE × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；PH 7.50
|
Resolution 2.20 Å R-free 0.265 |
| 1XM1 Nonbasic Thrombin Inhibitor Complex Deposited 2004-10-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
328–622（295 aa）
|
Not recorded | GAH N-{[(2S)-1-(N-{[4-({[AMINO(IMINO)METHYL]AMINO}METHYL)CYCLOHEXYL]CARBONYL}-3-CYCLOHEXYL-L-ALANYL)AZETIDIN-2-YL]CARBONYL}-L-TYROSYL-N~6~-[AMINO(IMINO)METHYL]-L-LYSINAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；0.1M potassium phosphate, 20%(w/v) PEG 6000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.30 Å R-free 0.266 |
| 1XMN Crystal structure of thrombin bound to heparin Deposited 2004-10-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 8 PDB declaration: octameric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
Chain C
328–363（36 aa）
Chain D
364–622（259 aa）
Chain E
328–363（36 aa）
Chain F
364–622（259 aa）
Chain G
328–363（36 aa）
Chain H
364–622（259 aa）
|
Not recorded | 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 4 NA SODIUM ION × 4 GOL GLYCEROL × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 3350, Sodium Citrate, glycerol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.85 Å R-free 0.234 |
| 1XMN Crystal structure of thrombin bound to heparin Deposited 2004-10-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
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 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 3350, Sodium Citrate, glycerol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.85 Å R-free 0.234 |
| 1XMN Crystal structure of thrombin bound to heparin Deposited 2004-10-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain G
328–363（36 aa）
Chain H
364–622（259 aa）
|
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 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 3350, Sodium Citrate, glycerol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.85 Å R-free 0.234 |
| 1XMN Crystal structure of thrombin bound to heparin Deposited 2004-10-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain E
328–363（36 aa）
Chain F
364–622（259 aa）
|
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 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 3350, Sodium Citrate, glycerol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.85 Å R-free 0.234 |
| 1XMN Crystal structure of thrombin bound to heparin Deposited 2004-10-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
328–363（36 aa）
Chain D
364–622（259 aa）
|
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 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 3350, Sodium Citrate, glycerol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.85 Å R-free 0.234 |
| 1YPE Thrombin Inhibitor Complex Deposited 2005-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Chain L
334–360（27 aa）
|
Not recorded | NA SODIUM ION × 2 UIP (1R,3AS,4R,8AS,8BR)-4-(2-BENZO[1,3]DIOXOL-5-YLMETHYL-1-ETHYL-3-OXO-DECAHYDRO-PYRROLO[3,4-A]PYRROLIZIN-4-YL)-BENZAMIDINE × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；phasphate buffer, sodium chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.81 Å R-free 0.235 |
| 1YPG Thrombin Inhibitor Complex Deposited 2005-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Chain L
334–360（27 aa）
|
Not recorded | UIR (1R,3AS,4R,8AS,8BR)-4-(2-BENZO[1,3]DIOXOL-5-YL-1-CYCLOPROPYL-3-OXO-DECAHYDRO-PYRROLO[3,4-A]PYRROLIZIN-4-YL)-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 1.80 Å R-free 0.248 |
| 1YPJ Thrombin Inhibitor Complex Deposited 2005-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Chain L
334–360（27 aa）
|
Not recorded | UIB (1R,3AS,4R,8AS,8BR)-4-{5-(PHENYL[1,3]DIOXOL-5-YLMETHYL)-4-ETHYL-2,3,3-TRIMETHYL-6-OXO-OCTAHYDRO-PYRROLO[3,4-C]PYRROL-1-YL}-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 1.78 Å R-free 0.239 |
| 1YPK Thrombin Inhibitor Complex Deposited 2005-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Chain L
334–360（27 aa）
|
Not recorded | CCR [N-[N-(4-METHOXY-2,3,6-TRIMETHYLPHENYLSULFONYL)-L-ASPARTYL]-D-(4-AMIDINO-PHENYLALANYL)]-PIPERIDINE × 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 1.78 Å R-free 0.239 |
| 1YPL X-ray crystal structure of thrombin inhibited by synthetic cyanopeptide analogue RA-1008 Deposited 2005-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Chain L
334–360（27 aa）
|
Not recorded | NA SODIUM ION × 2 RA8 N-(BENZYLSULFONYL)-L-LEUCYL-N-(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)-L-PROLINAMIDE × 1 GOL GLYCEROL × 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 1.85 Å R-free 0.263 |
| 1YPM X-ray crystal structure of thrombin inhibited by synthetic cyanopeptide analogue RA-1014 Deposited 2005-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Chain L
334–360（27 aa）
|
Not recorded | RA4 N-(4-NITROBENZOYL)-L-LEUCYL-N-(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)-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 1.85 Å R-free 0.260 |
| 1Z71 thrombin and P2 pyridine N-oxide inhibitor complex structure Deposited 2005-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
335–621（287 aa）
Fragment：alpha-thrombin
|
Not recorded | L17 L17 × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；peg8k, sodium phosphate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.80 Å R-free 0.254 |
| 1Z8I Crystal structure of the thrombin mutant G193A bound to PPACK Deposited 2005-03-30 | Different construct Different mutation/modification 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
324–361（38 aa）
Fragment：sequence database residues 324-361
Chain B
364–622（259 aa）
Fragment：sequence database residues 364-622
|
Mutation：G193A | ZN ZINC ION × 4 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, HANGING DROP；pH 7.4；298 K；20% PEG 8000, 0.1 M sodium cacodylate, 0.2 M zinc acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.242 |
| 1Z8J Crystal structure of the thrombin mutant G193P bound to PPACK Deposited 2005-03-30 | Different construct Different mutation/modification 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
322–361（40 aa）
Fragment：sequence database residues 322-361
Chain B
364–622（259 aa）
Fragment：sequence database residues 364-622
|
Mutation：G193P | ZN ZINC ION × 3 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, HANGING DROP；pH 7.4；298 K；20% PEG 8000, 0.1 M sodium cacodylate, 0.2 M zinc acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.246 |
| 1Z8J Crystal structure of the thrombin mutant G193P bound to PPACK Deposited 2005-03-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
322–361（40 aa）
Fragment：sequence database residues 322-361
Chain B
364–622（259 aa）
Fragment：sequence database residues 364-622
|
Mutation：G193P | ZN ZINC ION × 3 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, HANGING DROP；pH 7.4；298 K；20% PEG 8000, 0.1 M sodium cacodylate, 0.2 M zinc acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.246 |
| 1ZGI thrombin in complex with an oxazolopyridine inhibitor 21 Deposited 2005-04-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
335–621（287 aa）
Fragment：alpha-thrombin
|
Not recorded | 382 (R)-2-(2-(1H-1,2,4-TRIAZOL-1-YL)BENZYL)-N-(2,2-DIFLUORO-2-(PIPERIDIN-2-YL)ETHYL)OXAZOLO[4,5-C]PYRIDIN-4-AMINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEK8K, Sodium Phosphate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.20 Å R-free 0.264 |
| 1ZGV Thrombin in complex with an oxazolopyridine inhibitor 2 Deposited 2005-04-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
335–621（287 aa）
Fragment：alpha-thrombin
|
Not recorded | 501 N7-BUTYL-N2-(5-CHLORO-2-METHYLPHENYL)-5-METHYL[1,2,4]TRIAZOLO[1,5-A]PYRIMIDINE-2,7-DIAMINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEK8K, Sodium phosphate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.20 Å R-free 0.228 |
| 1ZRB Thrombin in complex with an azafluorenyl inhibitor 23b Deposited 2005-05-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
335–621（287 aa）
Fragment：alpha-thrombin
|
Not recorded | 062 3-AZA-9-HYDROXY-9-FLUORENYLCARBONYL-L-PROLYL-2-AMINOMETHYL-5-CHLOROBENZYLAMIDE, N-OXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 8000, sodium phosphate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.90 Å R-free 0.279 |
| 2A0Q Structure of thrombin in 400 mM potassium chloride Deposited 2005-06-16 | Different construct Different mutation/modification 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
334–363（30 aa）
Chain B
364–620（257 aa）
|
Mutation：R77A | NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；PEG-MME 2000, potassium chloride, Bis-Tris, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.240 |
| 2A0Q Structure of thrombin in 400 mM potassium chloride Deposited 2005-06-16 | Different construct Different mutation/modification 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
334–363（30 aa）
Chain D
364–620（257 aa）
|
Mutation：R77A | K POTASSIUM ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；PEG-MME 2000, potassium chloride, Bis-Tris, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.240 |
| 2A0Q Structure of thrombin in 400 mM potassium chloride Deposited 2005-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
334–363（30 aa）
Chain B
364–620（257 aa）
Chain C
334–363（30 aa）
Chain D
364–620（257 aa）
|
Mutation：R77A Mutation：R77A | NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 K POTASSIUM ION × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；PEG-MME 2000, potassium chloride, Bis-Tris, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.240 |
| 2A2X Orally Active Thrombin Inhibitors in Complex with Thrombin Inh12 Deposited 2005-06-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
330–363（34 aa）
|
Not recorded | NA9 N-(CARBOXYMETHYL)-3-CYCLOHEXYL-D-ALANYL-N-({6-[AMINO(IMINO)METHYL]PYRIDIN-3-YL}METHYL)-N~2~-METHYL-L-ALANINAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；PEG 400, Na-acetate, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.44 Å R-free 0.221 |
| 2A2X Orally Active Thrombin Inhibitors in Complex with Thrombin Inh12 Deposited 2005-06-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain H
364–622（259 aa）
Chain L
330–363（34 aa）
|
Not recorded | NA9 N-(CARBOXYMETHYL)-3-CYCLOHEXYL-D-ALANYL-N-({6-[AMINO(IMINO)METHYL]PYRIDIN-3-YL}METHYL)-N~2~-METHYL-L-ALANINAMIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；PEG 400, Na-acetate, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.44 Å R-free 0.221 |
| 2A45 Crystal structure of the complex between thrombin and the central "E" region of fibrin Deposited 2005-06-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
Chain D
328–363（36 aa）
Chain E
364–622（259 aa）
|
Not recorded | 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 2 PO4 PHOSPHATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICRODIALYSIS；pH 7.9；298 K；PEG 3500, AMMONIUM PHOSPHATE, TRIS, pH 7.90, MICRODIALYSIS, temperature 298K
|
Resolution 3.65 Å R-free 0.290 |
| 2AFQ 1.9 angstrom crystal structure of wild-type human thrombin in the sodium free state Deposited 2005-07-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
332–360（29 aa）
Fragment：Light Chain
Chain B
364–622（259 aa）
Fragment：Heavy Chain
Chain C
332–360（29 aa）
Fragment：Light Chain
Chain D
364–622（259 aa）
Fragment：Heavy Chain
|
Not recorded | GOL GLYCEROL × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG 3350, magnesium acetate, lithium chloride, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.93 Å R-free 0.229 |
| 2ANK orally active thrombin inhibitors in complex with thrombin and an exosite decapeptide Deposited 2005-08-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
330–363（34 aa）
|
Not recorded | N12 N-[(1R)-2-[(1-{[({6-[AMINO(IMINO)METHYL]PYRIDIN-3-YL}METHYL)AMINO]CARBONYL}CYCLOPENTYL)AMINO]-1-(CYCLOHEXYLMETHYL)-2-OXOETHYL]GLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；PEG 400, Na-acetate, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.46 Å R-free 0.211 |
| 2ANM Ternary complex of an orally active thrombin inhibitor with human thrombin and a c-terminal hirudin derived exo-sit inhibitor Deposited 2005-08-11 | Different construct Different mutation/modification 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
364–620（257 aa）
Fragment：Thrombin heavy chain
Chain L
328–363（36 aa）
Fragment：Thrombin light chain
|
Not recorded | CDO 2-((R)-1-((S)-2-(N-(6-CARBAMIMIDOYLPYRIDIN-3-YL)METHYLCARBAMOYL)-2H-PYRROL-1(5H)-YL)-3-CYCLOHEXYL-1-OXOPROPAN-2-YLAMINO)ACETIC ACID × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.40 Å R-free 0.250 |
| 2B5T 2.1 Angstrom structure of a nonproductive complex between antithrombin, synthetic heparin mimetic SR123781 and two S195A thrombin molecules Deposited 2005-09-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
315–363（49 aa）
Fragment：thrombin light chain
Chain B
364–622（259 aa）
Fragment：thrombin heavy chain, serine protease
Chain C
315–363（49 aa）
Fragment：thrombin light chain
Chain D
364–622（259 aa）
Fragment：thrombin heavy chain, serine protease
|
Mutation：S195A Mutation：S195A | GOL GLYCEROL × 12 SO4 SULFATE ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；PEG3350, glycerol, ammonium sulfate, (crystallized with NaCl and tris, but not in cryoprotectant), pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K
|
Resolution 2.10 Å R-free 0.247 |
| 2B5T 2.1 Angstrom structure of a nonproductive complex between antithrombin, synthetic heparin mimetic SR123781 and two S195A thrombin molecules Deposited 2005-09-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
315–363（49 aa）
Fragment：thrombin light chain
Chain B
364–622（259 aa）
Fragment：thrombin heavy chain, serine protease
Chain C
315–363（49 aa）
Fragment：thrombin light chain
Chain D
364–622（259 aa）
Fragment：thrombin heavy chain, serine protease
|
Mutation：S195A Mutation：S195A | GOL GLYCEROL × 12 SO4 SULFATE ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；PEG3350, glycerol, ammonium sulfate, (crystallized with NaCl and tris, but not in cryoprotectant), pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K
|
Resolution 2.10 Å R-free 0.247 |
| 2BVR Human thrombin complexed with fragment-based small molecules occupying the S1 pocket Deposited 2005-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–509（146 aa）
Fragment：LARGE SUBUNIT, RESIDUES 364-622
Chain H
516–622（107 aa）
Fragment：LARGE SUBUNIT, RESIDUES 364-622
Chain L
328–363（36 aa）
Fragment：SMALL SUBUNIT, RESIDUES 328-363
|
Not recorded | 4CP 2-[2-(4-CHLORO-PHENYLSULFANYL)-ACETYLAMINO]-3-(4-GUANIDINO-PHENYL)-PROPIONAMIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.25 Å R-free 0.229 |
| 2BVS Human thrombin complexed with fragment-based small molecules occupying the S1 pocket Deposited 2005-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：LARGE SUBUNIT, RESIDUES 364-622
Chain L
328–363（36 aa）
Fragment：SMALL SUBUNIT, RESIDUES 328-363
|
Not recorded | 2CE N-[2-(2-CARBAMOYLMETHOXY-ETHOXY)-ETHYL]-2-[2-(4-CHLORO-PHENYLSULFANYL)-ACETYLAMINO]-3-(4-GUANIDINO-PHENYL)-PROPIONAMIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.40 Å R-free 0.219 |
| 2BVX Design and Discovery of Novel, Potent Thrombin Inhibitors with a Solubilizing Cationic P1-P2-Linker Deposited 2005-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：LARGE SUBUNIT, RESIDUES 364-622
Chain L
328–363（36 aa）
Fragment：SMALL SUBUNIT, RESIDUES 328-363
|
Not recorded | 5CB N-(5-CHLORO-BENZO[B]THIOPHEN-3-YLMETHYL)-2-[6-CHLORO-OXO-3-(2-PYRIDIN-2-YL-ETHYLAMINO)-2H-PYRAZIN-1-YL]-ACETAMIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.20 Å R-free 0.306 |
| 2BXT Design and Discovery of Novel, Potent Thrombin Inhibitors with a Solubilizing Cationic P1-P2-Linker Deposited 2005-07-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：LARGE SUBUNIT, RESIDUES 364-622
Chain L
328–363（36 aa）
Fragment：SMALL SUBUNIT, RESIDUES 328-363
|
Not recorded | C2D 6-CHLORO-1-(2-{[(5-CHLORO-1-BENZOTHIEN-3-YL)METHYL]AMINO}ETHYL)-3-[(2-PYRIDIN-2-YLETHYL)AMINO]-1,4-DIHYDROPYRAZIN-2-OL × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.83 Å R-free 0.225 |
| 2BXU Design and Discovery of Novel, Potent Thrombin Inhibitors with a Solubilizing Cationic P1-P2-Linker Deposited 2005-07-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：LARGE SUBUNIT, RESIDUES 364-622
Chain L
328–363（36 aa）
Fragment：SMALL SUBUNIT, RESIDUES 328-363
|
Not recorded | C1D 1-(2-{[(6-AMINO-2-METHYLPYRIDIN-3-YL)METHYL]AMINO}ETHYL)-6-CHLORO-3-[(2,2-DIFLUORO-2-PYRIDIN-2-YLETHYL)AMINO]-1,4-DIHYDROPYRAZIN-2-OL × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.80 Å |
| 2C8W thrombin inhibitors Deposited 2005-12-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：FRAGMENT ALPHA THROMBIN, RESIDUES 328-363
Chain B
364–622（259 aa）
Fragment：FRAGMENT ALPHA THROMBIN, RESIDUES 364-622
|
Not recorded | NA SODIUM ION × 1 C7M (2S,3R)-N-[5-CHLORO-2-(2,3-DIHYDRO-1H-TETRAZOL-1-YL)BENZYL]-3-HYDROXY-4-{[(4-METHOXYPHENYL)SULFONYL]AMINO}-1-PHENYLBUTA N-2-AMINIUM × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.3；PH 7.30
|
Resolution 1.96 Å R-free 0.219 |
| 2C8X thrombin inhibitors Deposited 2005-12-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：FRAGMENT ALPHA THROMBIN, RESIDUES 328-363
Chain B
364–622（259 aa）
Fragment：FRAGMENT ALPHA THROMBIN, RESIDUES 364-622
|
Not recorded | DMS DIMETHYL SULFOXIDE × 2 NA SODIUM ION × 1 C5M N-{(2R,3S)-3-[(3-CHLOROBENZYL)AMINO]-2-HYDROXY-4-PHENYLBUTYL}-4-METHOXY-2,3,6-TRIMETHYLBENZENESULFONAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.3；PH 7.30
|
Resolution 2.17 Å R-free 0.229 |
| 2C8Y thrombin inhibitors Deposited 2005-12-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：FRAGMENT ALPHA THROMBIN, RESIDUES 328-363
Chain B
364–622（259 aa）
Fragment：FRAGMENT ALPHA THROMBIN, RESIDUES 364-622
|
Not recorded | DMS DIMETHYL SULFOXIDE × 3 NA SODIUM ION × 1 C3M N-[(2R,3S)-3-AMINO-2-HYDROXY-4-PHENYLBUTYL]NAPHTHALENE-2-SULFONAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.3；PH 7.30
|
Resolution 2.20 Å R-free 0.259 |
| 2C8Z thrombin inhibitors Deposited 2005-12-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：FRAGMENT ALPHA THROMBIN, RESIDUES 328-363
Chain B
364–622（259 aa）
Fragment：FRAGMENT ALPHA THROMBIN, RESIDUES 364-622
|
Not recorded | NA SODIUM ION × 1 DMS DIMETHYL SULFOXIDE × 1 C2A 1-(3-CHLOROPHENYL)METHANAMINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.3；PH 7.30
|
Resolution 2.14 Å R-free 0.246 |
| 2C90 thrombin inhibitors Deposited 2005-12-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：FRAGMENT ALPHA THROMBIN, RESIDUES 328-363
Chain B
364–622（259 aa）
Fragment：FRAGMENT ALPHA THROMBIN, RESIDUES 364-622
|
Not recorded | DMS DIMETHYL SULFOXIDE × 1 NA SODIUM ION × 1 C1M 1-(4-CHLOROPHENYL)-1H-TETRAZOLE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.3；PH 7.30
|
Resolution 2.25 Å R-free 0.306 |
| 2C93 thrombin inhibitors Deposited 2005-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：FRAGMENT ALPHA THROMBIN, RESIDUES 328-363
Chain B
364–622（259 aa）
Fragment：FRAGMENT ALPHA THROMBIN, RESIDUES 364-622
|
Not recorded | DMS DIMETHYL SULFOXIDE × 2 NA SODIUM ION × 1 C4M N-[(2R,3S)-3-AMINO-2-HYDROXY-4-PHENYLBUTYL]-4-METHOXY-2,3,6-TRIMETHYLBENZENESULFONAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.3；PH 7.30
|
Resolution 2.20 Å R-free 0.242 |
| 2CF8 Complex of recombinant human thrombin with an inhibitor Deposited 2006-02-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Fragment：CATALYTIC, RESIDUES 364-620
Chain L
334–361（28 aa）
Fragment：LIGHT CHAIN, RESIDUES 334-361
|
Not recorded | ESH 4- [(1R,3AS,4R,8AS,8BR)- 2- (4-CHLOROBENZYL)- 1- ISOPROPYL- 3- OXODECAHYDROPYRROLO[3,4- A]PYRROLIZIN- 4- YL]BENZENECARBOXIMIDAMIDE × 1 NA SODIUM ION × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.4；PH 7.40
|
Resolution 1.30 Å R-free 0.199 |
| 2CF9 Complex of recombinant human thrombin with an inhibitor Deposited 2006-02-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Fragment：CATALYTIC, RESIDUES 364-620
Chain L
334–361（28 aa）
Fragment：LIGHT CHAIN, RESIDUES 334-361
|
Not recorded | 348 4-[(1R,3AS,4R,8AS,8BR)-1-ISOPROPYL-2-(4-METHOXYBENZYL)-3-OXODECAHYDROPYRROLO[3,4-A]PYRROLIZIN-4-YL]BENZENECARBOXIMIDAMIDE × 1 NA SODIUM ION × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.4；PH 7.40
|
Resolution 1.79 Å R-free 0.198 |
| 2CN0 Complex of Recombinant Human Thrombin with a Designed Inhibitor Deposited 2006-05-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Fragment：RESIDUES 364-620
Chain L
334–361（28 aa）
Fragment：RESIDUES 334-361
|
Not recorded | F25 4-(1R,3AS,4R,8AS,8BR)-[1-DIFLUOROMETHYL-2-(4-FLUOROBENZYL)-3-OXODECAHYDROPYRROLO[3,4-A]PYRROLIZIN-4-YL]BENZAMIDINE × 1 NA SODIUM ION × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.4；PH 7.40
|
Resolution 1.30 Å R-free 0.204 |
| 2FEQ orally active thrombin inhibitors Deposited 2005-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 34P N-(CARBOXYMETHYL)-3-CYCLOHEXYL-D-ALANYL-N-({4-[(E)-AMINO(IMINO)METHYL]-1,3-THIAZOL-2-YL}METHYL)-L-PROLINAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 8.5；298 K；PEG 8000, Na-acetate, Tris, pH 8.5, EVAPORATION, temperature 298.0K
|
Resolution 2.44 Å R-free 0.242 |
| 2FEQ orally active thrombin inhibitors Deposited 2005-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 34P N-(CARBOXYMETHYL)-3-CYCLOHEXYL-D-ALANYL-N-({4-[(E)-AMINO(IMINO)METHYL]-1,3-THIAZOL-2-YL}METHYL)-L-PROLINAMIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 8.5；298 K；PEG 8000, Na-acetate, Tris, pH 8.5, EVAPORATION, temperature 298.0K
|
Resolution 2.44 Å R-free 0.242 |
| 2FES Orally active thrombin inhibitors Deposited 2005-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 3SP N-(CARBOXYMETHYL)-3-CYCLOHEXYL-D-ALANYL-N-({5-[(E)-AMINO(IMINO)METHYL]THIEN-2-YL}METHYL)-L-PROLINAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；PEG 8000, Na-acetet, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.42 Å R-free 0.220 |
| 2GDE Thrombin in complex with inhibitor Deposited 2006-03-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 1 SN3 (R)-3-((2S,3R)-1-((2S,3AR,5S,6S,7AS)-2-(2-(1-CARBAMIMIDOYL-2,5-DIHYDRO-1H-PYRROL-3-YL)ETHYLCARBAMOYL)-5,6-DIHYDROXYOCTA HYDRO-1H-INDOL-1-YL)-3-CHLORO-4-METHYL-1-OXOPENTAN-2-YLAMINO)-2-METHOXY-3-OXOPROPYL HYDROGEN SULFATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.248 |
| 2GP9 Crystal structure of the slow form of thrombin in a self-inhibited conformation Deposited 2006-04-17 | Different construct Different mutation/modification 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
328–363（36 aa）
Fragment：THROMBIN LIGHT CHAIN
Chain B
364–622（259 aa）
Fragment：THROMBIN heavy CHAIN
|
Mutation：D102N | EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；18% PEG 20000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
|
Resolution 1.87 Å R-free 0.218 |
| 2H9T Crystal structure of human alpha-thrombin in complex with suramin Deposited 2006-06-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：heavy chain, residues 364-622
Chain L
328–363（36 aa）
Fragment：light chain, residues 328-363
|
Not recorded | SVR 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；100 mM tris, 25 % tert-butanol, 0.16 mM thrombin:suramin complex, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.40 Å R-free 0.266 |
| 2HGT STRUCTURE OF THE HIRUGEN AND HIRULOG 1 COMPLEXES OF ALPHA-THROMBIN Deposited 1991-06-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.20 Å |
| 2HNT CRYSTALLOGRAPHIC STRUCTURE OF HUMAN GAMMA-THROMBIN Deposited 1994-08-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain C
364–433（70 aa）
Chain E
437–517（81 aa）
Chain F
518–622（105 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.50 Å |
| 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：UNP residues 364-622
Chain L
328–363（36 aa）
Fragment：UNP residues 328-363
|
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 |
| 2HPQ 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
Chain P
213–291（79 aa）
Fragment：Activation peptide fragment 2
|
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 |
| 2HWL Crystal structure of thrombin in complex with fibrinogen gamma' peptide Deposited 2006-08-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
328–363（36 aa）
Fragment：Thrombin light chain
Chain B
364–622（259 aa）
Fragment：Thrombin heavy chain
Chain C
328–363（36 aa）
Fragment：Thrombin light chain
Chain D
364–622（259 aa）
Fragment：Thrombin heavy chain
|
Mutation：R77AA Mutation：R77AA | NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25% PEG 4000, 100 mM HEPES sodium salt buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.40 Å R-free 0.249 |
| 2JH0 Human Thrombin Hirugen Inhibitor complex Deposited 2007-02-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
328–363（36 aa）
Fragment：LIGHT CHAIN, RESIDUES 328-363
Chain D
364–622（259 aa）
Fragment：HEAVY CHAIN, RESIDUES 364-622
|
Not recorded | 701 (2R)-2-(5-CHLORO-2-THIENYL)-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-OXOETHYL]-2-OXOPYRROLIDIN-3-YL}PROPENE-1-SULFONAMIDE × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.8；PH 6.80
|
Resolution 1.70 Å R-free 0.210 |
| 2JH5 Human Thrombin Hirugen Inhibitor complex Deposited 2007-02-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
328–363（36 aa）
Fragment：LIGHT CHAIN, RESIDUES 328-363
Chain D
364–622（259 aa）
Fragment：HEAVY CHAIN, RESIDUES 364-622
|
Not recorded | CA CALCIUM ION × 1 NA SODIUM ION × 1 895 2-(5-CHLORO-2-THIENYL)-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-OXOETHYL]-2-OXOPYRROLIDIN-3-YL}ETHENESULFONAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.8；PH 6.80
|
Resolution 2.50 Å R-free 0.231 |
| 2JH6 Human Thrombin Hirugen Inhibitor complex Deposited 2007-02-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
328–363（36 aa）
Fragment：LIGHT CHAIN, RESIDUES 328-363
Chain D
364–622（259 aa）
Fragment：HEAVY CHAIN, RESIDUES 364-622
|
Not recorded | CA CALCIUM ION × 1 NA SODIUM ION × 1 894 2-(5-CHLORO-2-THIENYL)-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-OXOETHYL]-2-OXOPYRROLIDIN-3-YL}ETHANESULFONAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.8；PH 6.80
|
Resolution 2.21 Å R-free 0.196 |
| 2OD3 Human thrombin chimera with human residues 184a, 186, 186a, 186b, 186c and 222 replaced by murine thrombin equivalents. Deposited 2006-12-21 | Different construct Different mutation/modification 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
328–363（36 aa）
Chain B
364–622（259 aa）
|
Mutation：Y184aF, P186V, D186aN, E186bD, G186cT, D222K | 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 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；20% PEG 3350, 0.2M lithium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.75 Å R-free 0.230 |
| 2PGB Inhibitor-free human thrombin mutant C191A-C220A Deposited 2007-04-09 | Different construct Different mutation/modification 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
328–363（36 aa）
Fragment：Thrombin light chain, 328-363
Chain B
364–622（259 aa）
Fragment：Thrombin heavy chain, 364-622
|
Mutation：C191A, C220A | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；25% PEG 4000, 0.2 M Lithium Sulfate and 0.1 M TRIS- HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.54 Å R-free 0.217 |
| 2PGQ Human thrombin mutant C191A-C220A in complex with the inhibitor PPACK Deposited 2007-04-10 | Different construct Different mutation/modification 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
319–363（45 aa）
Fragment：residues 319-363
Chain B
364–622（259 aa）
Fragment：residues 364-622
|
Mutation：C191A, C220A | ZN ZINC ION × 3 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 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；295 K；20% PEG 3350 and 0.2 M Zinc Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.3
|
Resolution 1.80 Å R-free 0.222 |
| 2PKS Thrombin in complex with inhibitor Deposited 2007-04-18 | 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 A
334–360（27 aa）
Fragment：Residues 335-361
Chain B
364–510（147 aa）
Fragment：Residues 364-510
Chain C
518–619（102 aa）
Fragment：Residues 518-619
|
Not recorded | NA SODIUM ION × 1 G44 4-({[4-(3-METHYLBENZOYL)PYRIDIN-2-YL]AMINO}METHYL)BENZENECARBOXIMIDAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；27% PEG8000, 0.1M SODIUM PHOSPHATE, PH 7.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
|
Resolution 2.50 Å R-free 0.259 |
| 2PW8 Crystal structure of sulfo-hirudin complexed to thrombin Deposited 2007-05-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Chain L
334–360（27 aa）
|
Not recorded | 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 |
| 2R2M 2-(2-Chloro-6-Fluorophenyl)Acetamides as Potent Thrombin Inhibitors Deposited 2007-08-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–359（26 aa）
Fragment：unp residues 334-359
Chain B
364–622（259 aa）
|
Not recorded | I50 N-[2-({[amino(imino)methyl]amino}oxy)ethyl]-2-{6-chloro-3-[(2,2-difluoro-2-phenylethyl)amino]-2-fluorophenyl}acetamide × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.10 Å R-free 0.214 |
| 2THF STRUCTURE OF HUMAN ALPHA-THROMBIN Y225F MUTANT BOUND TO D-PHE-PRO-ARG-CHLOROMETHYLKETONE Deposited 1999-01-26 | Different construct Different mutation/modification 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
328–363（36 aa）
Chain B
364–622（259 aa）
|
Mutation：Y225F | 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
pH 7.5；pH 7.5
|
Resolution 2.10 Å R-free 0.265 |
| 2UUF Thrombin-hirugen binary complex at 1.26A resolution Deposited 2007-03-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：RESIDUES 328-363
Chain B
364–622（259 aa）
Fragment：RESIDUES 364-622
|
Not recorded | NA SODIUM ION × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；CRYSTALS WERE GROWN BY MACROSEEDING A SOLUTION OF 100MM HEPES PH 7.0, 28% PEG4K, 500MM NACL.
|
Resolution 1.26 Å R-free 0.194 |
| 2UUJ Thrombin-hirugen-gw473178 ternary complex at 1.32A resolution Deposited 2007-03-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：RESIDUES 328-363
Chain B
364–622（259 aa）
Fragment：RESIDUES 364-622
|
Not recorded | NA SODIUM ION × 1 CA CALCIUM ION × 1 896 N-ETHYL-N-ISOPROPYL-3-METHYL-5-{[(2S)-2-(PYRIDIN-4-YLAMINO)PROPYL]OXY}BENZAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN BY MACROSEEDING A SOLUTION OF 100MM HEPES PH 7.0, 28% PEG4K, 500MM NACL.
|
Resolution 1.32 Å R-free 0.211 |
| 2UUK Thrombin-hirugen-gw420128 ternary complex at 1.39A resolution Deposited 2007-03-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：RESIDUES 328-363
Chain B
364–622（259 aa）
Fragment：RESIDUES 364-622
|
Not recorded | NA SODIUM ION × 1 CA CALCIUM ION × 1 897 N-[3-(TERT-BUTYLAMINO)-3-OXOPROPYL]-N-ISOPROPYL-3-METHYL-5-{[(2S)-2-(PYRIDIN-4-YLAMINO)PROPYL]OXY}BENZAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN BY MACROSEEDING A SOLUTION OF 100MM HEPES PH 7.0, 28% PEG4K,500MM NACL.
|
Resolution 1.39 Å R-free 0.173 |
| 2V3H Thrombin with 3-cycle no F Deposited 2007-06-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Fragment：CATALYTIC, RESIDUES 364-620
Chain L
334–361（28 aa）
Fragment：LIGHT CHAIN, RESIDUES 334-361
|
Not recorded | I25 (2R)-({4-[AMINO(IMINO)METHYL]PHENYL}AMINO){3-[3-(DIMETHYLAMINO)-2,2-DIMETHYLPROPOXY]-5-ETHYLPHENYL}ACETIC 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 0.207 |
| 2V3O Thrombin with 3-cycle with F Deposited 2007-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Fragment：CATALYTIC, RESIDUES 364-620
Chain L
334–361（28 aa）
Fragment：LIGHT CHAIN, RESIDUES 334-361
|
Not recorded | 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 |
| 2ZFQ Exploring thrombin S3 pocket Deposited 2008-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 45U (S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclopentyloxy)ethanoyl)pyrrolidine-2-carboxamide × 1 BEN BENZAMIDINE × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate buffer, sodium chloride, PEG8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.80 Å R-free 0.245 |
| 2ZFR Exploring thrombin S3 pocket Deposited 2008-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 46U (S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclohexyloxy)ethanoyl)pyrrolidine-2-carboxamide × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate buffer, sodium chloride, PEG8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.85 Å R-free 0.253 |
| 2ZG0 Exploring thrombin S3 pocket Deposited 2008-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 50U (S)-N-(4-carbamimidoylbenzyl)-1-(3-cyclohexylpropanoyl)pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate buffer, sodium chloride, PEG8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.75 Å R-free 0.243 |
| 2ZGB Thrombin Inhibition Deposited 2008-01-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 |
| 2ZHE Exploring thrombin S3 pocket Deposited 2008-02-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 13U N-cyclooctylglycyl-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, PEG8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.10 Å R-free 0.298 |
| 2ZHF Exploring thrombin S3 pocket Deposited 2008-02-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 49U (S)-N-(4-carbamimidoylbenzyl)-1-(3-cyclopentylpropanoyl)pyrrolidine-2-carboxamide × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Phosphate buffer, sodium chloride, PEG8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.98 Å R-free 0.261 |
| 2ZHQ Thrombin Inhibition Deposited 2008-02-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 |
| 2ZHW Exploring thrombin S3 pocket Deposited 2008-02-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 12U N-cycloheptylglycyl-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, PEG8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.02 Å R-free 0.292 |
| 2ZI2 Thrombin Inhibition Deposited 2008-02-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 |
| 3B23 Crystal structure of thrombin-variegin complex: Insights of a novel mechanism of inhibition and design of tunable thrombin inhibitors Deposited 2011-07-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；100mM HEPES buffer pH 7.4, 20-25% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.40 Å R-free 0.259 |
| 3B9F 1.6 A structure of the PCI-thrombin-heparin complex Deposited 2007-11-05 | Different construct 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 H
364–622（259 aa）
Fragment：Thrombin heavy chain
Chain L
315–363（49 aa）
Fragment：Thrombin light chain
|
Mutation：S195A (chymotrypsin numbering) | SO4 SULFATE ION × 3 GOL GLYCEROL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；11% PEG 3350, 0.12M MgSO4, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.60 Å R-free 0.234 |
| 3BEF Crystal structure of thrombin bound to the extracellular fragment of PAR1 Deposited 2007-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
320–363（44 aa）
Fragment：THROMBIN LIGHT CHAIN
Chain B
364–622（259 aa）
Fragment：THROMBIN HEAVY CHAIN
|
Mutation：D102N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 30% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
|
Resolution 2.20 Å R-free 0.248 |
| 3BEF Crystal structure of thrombin bound to the extracellular fragment of PAR1 Deposited 2007-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
320–363（44 aa）
Fragment：THROMBIN LIGHT CHAIN
Chain E
364–622（259 aa）
Fragment：THROMBIN HEAVY CHAIN
|
Mutation：D102N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 30% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
|
Resolution 2.20 Å R-free 0.248 |
| 3BEI Crystal structure of the slow form of thrombin in a self_inhibited conformation Deposited 2007-11-19 | Different construct Different mutation/modification 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
320–363（44 aa）
Fragment：THROMBIN LIGHT CHAIN
Chain B
364–622（259 aa）
Fragment：THROMBIN HEAVY CHAIN
|
Mutation：D102N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；12.5% PEG 4000, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.55 Å R-free 0.215 |
| 3BF6 Thrombin:suramin complex Deposited 2007-11-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：HEAVY CHAIN, RESIDUES 364-622
Chain L
328–363（36 aa）
Fragment：LIGHT CHAIN, RESIDUES 328-363
|
Not recorded | SVR 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；100 mM Tris, 25% v/v t-butanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.50 Å R-free 0.282 |
| 3BIU Human thrombin-in complex with UB-THR10 Deposited 2007-12-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Chain L
333–361（29 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 10U (S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclopentylamino)ethanoyl)pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；phosphate buffer, sodium chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.30 Å R-free 0.263 |
| 3BIV Human thrombin-in complex with UB-THR11 Deposited 2007-12-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Chain L
333–361（29 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 11U (S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclohexylamino)ethanoyl)pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；phosphate buffer, sodium chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.80 Å R-free 0.264 |
| 3BV9 Structure of Thrombin Bound to the Inhibitor FM19 Deposited 2008-01-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–363（31 aa）
Chain B
364–622（259 aa）
|
Mutation：R(77a)A | IOD IODIDE ION × 3 NA SODIUM ION × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；20% PEG 3350, 100 mM Bis/Tris, 200 mM NaI, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
|
Resolution 1.80 Å R-free 0.239 |
| 3C1K Crystal structure of thrombin in complex with inhibitor 15 Deposited 2008-01-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
335–621（287 aa）
Fragment：alpha-thrombin, Peptidase S1
|
Not recorded | T15 2-{3-[(benzylsulfonyl)amino]-6-methyl-2-oxopyridin-1(2H)-yl}-N-({1-[2-(tert-butylamino)-2-oxoethyl]-4-methyl-1H-imidazol-5-yl}methyl)acetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEK8K, Sodium phosphate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.84 Å |
| 3C27 Cyanofluorophenylacetamides as Orally Efficacious Thrombin Inhibitors Deposited 2008-01-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–359（26 aa）
Fragment：unp residues 334-359
Chain B
364–622（259 aa）
Fragment：UNP residues 364-622
|
Not recorded | DKK N-[2-(carbamimidamidooxy)ethyl]-2-{6-cyano-3-[(2,2-difluoro-2-pyridin-2-ylethyl)amino]-2-fluorophenyl}acetamide × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.18 Å R-free 0.215 |
| 3D49 Thrombin Inhibition Deposited 2008-05-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 |
| 3DA9 Crystal structure of thrombin in complex with inhibitor Deposited 2008-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：UNP residues 328-363
Chain B
364–622（259 aa）
Fragment：UNP residues 364-622
|
Not recorded | NA SODIUM ION × 1 44U beta-phenyl-D-phenylalanyl-N-propyl-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；The drop was made by mixing 1.5 ul of the thrombin-hirudin complex and 1.5 ul of reservior solution containing: Phosphate buffer pH7.3, 28% PEG, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.80 Å R-free 0.215 |
| 3DD2 Crystal structure of an RNA aptamer bound to human thrombin Deposited 2008-06-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Chain L
332–361（30 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 3 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 MG MAGNESIUM ION × 2 P6G HEXAETHYLENE GLYCOL × 1 ACY ACETIC ACID × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；PEG 8000, Magnesium Acetate, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
|
Resolution 1.90 Å R-free 0.254 |
| 3DHK Bisphenylic Thrombin Inhibitors Deposited 2008-06-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 |
| 3E6P Crystal structure of human meizothrombin desF1 Deposited 2008-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain H
364–622（259 aa）
Fragment：Thrombin heavy chain: UNP residues 364-622
Chain L
206–363（158 aa）
Fragment：Activation peptide fragment 2 and thrombin light chain: UNP residues 206-363
|
Not recorded | SO4 SULFATE ION × 1 DFK D-PHENYLALANYL-N-[(1S)-4-{[(Z)-AMINO(IMINO)METHYL]AMINO}-1-(CHLOROACETYL)BUTYL]-L-PROLINAMIDE × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.6；295 K；0.2M Na2(SO4), 23% PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.10 Å R-free 0.249 |
| 3EE0 Crystal Structure of the W215A/E217A Mutant of Human Thrombin (space group P2(1)2(1)2(1)) Deposited 2008-09-03 | Different construct Different mutation/modification 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
328–363（36 aa）
Chain B
364–622（259 aa）
|
Mutation：W215A, E217A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1M MES, 30% PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.75 Å R-free 0.323 |
| 3EGK KNOBLE Inhibitor Deposited 2008-09-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 |
| 3F68 Thrombin Inhibition Deposited 2008-11-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：UNP residues 364-622, Thrombin heavy chain
Chain L
328–363（36 aa）
Fragment：UNP residues 328-363, Thrombin light chain
|
Not recorded | 91U N-acetyl-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 1.75 Å R-free 0.256 |
| 3GIC Structure of thrombin mutant delta(146-149e) in the free form Deposited 2009-03-05 | Different construct Different mutation/modification 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
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% PEG 20000, 100 mM Tris buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.55 Å R-free 0.220 |
| 3GIS Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin Deposited 2009-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
315–363（49 aa）
Fragment：Thrombin light-chain, UNP residues 315-363
Chain B
364–622（259 aa）
Fragment：Thrombin heavy-chain, UNP residues 364-622
|
Mutation：S195A | SO4 SULFATE ION × 7 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；294 K；0.2M LiSO4, 22% PEG3350, pH7.0, vapor diffusion, temperature 294K, VAPOR DIFFUSION
|
Resolution 2.40 Å R-free 0.259 |
| 3GIS Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin Deposited 2009-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
315–363（49 aa）
Fragment：Thrombin light-chain, UNP residues 315-363
Chain D
364–622（259 aa）
Fragment：Thrombin heavy-chain, UNP residues 364-622
|
Mutation：S195A | SO4 SULFATE ION × 5 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；294 K；0.2M LiSO4, 22% PEG3350, pH7.0, vapor diffusion, temperature 294K, VAPOR DIFFUSION
|
Resolution 2.40 Å R-free 0.259 |
| 3GIS Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin Deposited 2009-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
315–363（49 aa）
Fragment：Thrombin light-chain, UNP residues 315-363
Chain F
364–622（259 aa）
Fragment：Thrombin heavy-chain, UNP residues 364-622
|
Mutation：S195A | SO4 SULFATE ION × 3 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；294 K；0.2M LiSO4, 22% PEG3350, pH7.0, vapor diffusion, temperature 294K, VAPOR DIFFUSION
|
Resolution 2.40 Å R-free 0.259 |
| 3HAT ACTIVE SITE MIMETIC INHIBITION OF THROMBIN Deposited 1994-10-16 | 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 H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.50 Å |
| 3HKJ Crystal structure of human thrombin mutant W215A/E217A in complex with the extracellular fragment of human PAR1 Deposited 2009-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–363（31 aa）
Fragment：Light chain: UNP residues 333-363
Chain B
364–622（259 aa）
Fragment：Heavy chain: UNP residues 364-622
|
Mutation：W215A, E217A | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；100mM HEPES pH 7.5, 20% PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.60 Å R-free 0.234 |
| 3HKJ Crystal structure of human thrombin mutant W215A/E217A in complex with the extracellular fragment of human PAR1 Deposited 2009-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
333–363（31 aa）
Fragment：Light chain: UNP residues 333-363
Chain E
364–622（259 aa）
Fragment：Heavy chain: UNP residues 364-622
|
Mutation：W215A, E217A | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；100mM HEPES pH 7.5, 20% PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.60 Å R-free 0.234 |
| 3HTC THE STRUCTURE OF A COMPLEX OF RECOMBINANT HIRUDIN AND HUMAN ALPHA-THROMBIN Deposited 1993-06-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å |
| 3JZ1 Crystal structure of human thrombin mutant N143P in E:Na+ form Deposited 2009-09-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Mutation：N143P | NA SODIUM ION × 4 NO3 NITRATE ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.8；295 K；0.2M NaNO3 and 20% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.60 Å R-free 0.216 |
| 3JZ1 Crystal structure of human thrombin mutant N143P in E:Na+ form Deposited 2009-09-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Mutation：N143P | NA SODIUM ION × 2 NO3 NITRATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.8；295 K；0.2M NaNO3 and 20% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.60 Å R-free 0.216 |
| 3JZ2 Crystal structure of human thrombin mutant N143P in E* form Deposited 2009-09-22 | Different construct Different mutation/modification 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
328–363（36 aa）
Chain B
364–622（259 aa）
|
Mutation：N143P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；0.1M imidazole and 7% PEG 8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.40 Å R-free 0.246 |
| 3K65 Crystal Structure of Prethombin-2/Fragment-2 Complex Deposited 2009-10-08 | Different construct Different mutation/modification 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
199–314（116 aa）
Fragment：residues 199-314
Chain B
315–622（308 aa）
Fragment：residues 315-622
|
Mutation：S525A | BU1 1,4-BUTANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；10% Buffer 1 mix, 10% Alcohols mix, 40% EDO-P8K mix, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.85 Å R-free 0.229 |
| 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
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 |
| 3LU9 Crystal structure of human thrombin mutant S195A in complex with the extracellular fragment of human PAR1 Deposited 2010-02-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
318–363（46 aa）
Chain B
364–622（259 aa）
|
Mutation：S195A | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.2；295 K；200mM K/Na tartrate, 20% PEG3350, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.80 Å R-free 0.236 |
| 3LU9 Crystal structure of human thrombin mutant S195A in complex with the extracellular fragment of human PAR1 Deposited 2010-02-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
318–363（46 aa）
Chain E
364–622（259 aa）
|
Mutation：S195A | 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 7.2；295 K；200mM K/Na tartrate, 20% PEG3350, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.80 Å R-free 0.236 |
| 3NXP Crystal structure of human prethrombin-1 Deposited 2010-07-14 | 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
199–622（424 aa）
Fragment：UNP residues 199-622
|
Mutation：R271A, R284A | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；100mM Tris-HCl, pH 8.5 and 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.20 Å R-free 0.226 |
| 3P17 Thrombin Inhibition by Pyridin Derivatives Deposited 2010-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 99P D-phenylalanyl-N-(pyridin-3-ylmethyl)-L-prolinamide × 1 PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG 8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.43 Å R-free 0.176 |
| 3P6Z Structural basis of thrombin mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction Deposited 2010-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：THROMBIN LIGHT CHAIN
Chain B
364–622（259 aa）
Fragment：THROMBIN HEAVY CHAIN
|
Not recorded | NA SODIUM ION × 3 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 CL CHLORIDE ION × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM MOPS/HEPES-Na, pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) 2-methylpentane-2,4-diol (MPD), 30 mM Ca2+, 30 mM Mg2+, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.239 |
| 3P6Z Structural basis of thrombin mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction Deposited 2010-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
328–363（36 aa）
Fragment：THROMBIN LIGHT CHAIN
Chain H
364–622（259 aa）
Fragment：THROMBIN HEAVY CHAIN
|
Not recorded | NA SODIUM ION × 6 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 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM MOPS/HEPES-Na, pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) 2-methylpentane-2,4-diol (MPD), 30 mM Ca2+, 30 mM Mg2+, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.239 |
| 3P70 Structural basis of thrombin-mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction Deposited 2010-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Fragment：THROMBIN LIGHT CHAIN
Chain B
364–622（259 aa）
Fragment：THROMBIN HEAVY CHAIN
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 BEN BENZAMIDINE × 1 NA SODIUM ION × 2 BGC beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM MOPS/HEPES-Na, pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) 2-methylpentane-2,4-diol (MPD), 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine , VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.55 Å R-free 0.279 |
| 3P70 Structural basis of thrombin-mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction Deposited 2010-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
328–363（36 aa）
Fragment：THROMBIN LIGHT CHAIN
Chain D
364–622（259 aa）
Fragment：THROMBIN HEAVY CHAIN
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 BEN BENZAMIDINE × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM MOPS/HEPES-Na, pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) 2-methylpentane-2,4-diol (MPD), 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine , VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.55 Å R-free 0.279 |
| 3P70 Structural basis of thrombin-mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction Deposited 2010-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
328–363（36 aa）
Fragment：THROMBIN LIGHT CHAIN
Chain F
364–622（259 aa）
Fragment：THROMBIN HEAVY CHAIN
|
Not recorded | BEN BENZAMIDINE × 1 NA SODIUM ION × 1 BGC beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM MOPS/HEPES-Na, pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) 2-methylpentane-2,4-diol (MPD), 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine , VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.55 Å R-free 0.279 |
| 3P70 Structural basis of thrombin-mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction Deposited 2010-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
328–363（36 aa）
Fragment：THROMBIN LIGHT CHAIN
Chain H
364–622（259 aa）
Fragment：THROMBIN HEAVY CHAIN
|
Not recorded | BEN BENZAMIDINE × 1 NA SODIUM ION × 2 BGC beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM MOPS/HEPES-Na, pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) 2-methylpentane-2,4-diol (MPD), 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine , VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.55 Å R-free 0.279 |
| 3PMH Mechanism of Sulfotyrosine-Mediated Glycoprotein Ib Interaction with Two Distinct alpha-Thrombin Sites Deposited 2010-11-16 | Different construct 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 A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | 0G7 D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-prolinamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；277 K；16% PEG 6000, 0.2M ammonium phosphate, pH 7.0, VAPOR DIFFUSION, temperature 277K
|
Resolution 3.20 Å R-free 0.263 |
| 3PO1 Thrombin in complex with Benzothiazole Guanidine Deposited 2010-11-21 | 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 A
334–360（27 aa）
Chain B
364–510（147 aa）
Chain C
518–619（102 aa）
|
Not recorded | MKY ethyl [(2Z)-2-(carbamimidoylimino)-6-hydroxy-1,3-benzothiazol-3(2H)-yl]acetate × 1 NA SODIUM ION × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 7.3；298 K；0.05 M sodium phosphate, 28% PEG8000, pH 7.3, EVAPORATION, temperature 298K
|
Resolution 1.65 Å R-free 0.260 |
| 3QDZ Crystal structure of the human thrombin mutant D102N in complex with the extracellular fragment of human PAR4. Deposited 2011-01-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–363（31 aa）
Chain B
364–622（259 aa）
|
Mutation：D102N | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；1.6 M tri-sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.80 Å R-free 0.364 |
| 3QDZ Crystal structure of the human thrombin mutant D102N in complex with the extracellular fragment of human PAR4. Deposited 2011-01-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
333–363（31 aa）
Chain D
364–622（259 aa）
|
Mutation：D102N | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；1.6 M tri-sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.80 Å R-free 0.364 |
| 3QGN The allosteric E*-E equilibrium is a key property of the trypsin fold Deposited 2011-01-24 | Different construct Different mutation/modification 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
333–363（31 aa）
Fragment：unp residues 333-363
Chain B
364–622（259 aa）
Fragment：unp residues 364-622
|
Mutation：N143P | IOD IODIDE ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.2；295 K；0.2 M NH4I and 20 % PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.10 Å R-free 0.239 |
| 3QLP X-ray structure of the complex between human alpha thrombin and a modified thrombin binding aptamer (mTBA) Deposited 2011-02-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
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 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；20% w/v PEG 20000, 0.2M ammonium sulfate, 3% n-propanol, 0.1 M sodium acetate pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.14 Å R-free 0.237 |
| 3QTO Thrombin Inhibition by Pyridin Derivatives Deposited 2011-02-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 10P D-phenylalanyl-N-[(1-methylpyridinium-3-yl)methyl]-L-prolinamide × 1 GOL GLYCEROL × 1 PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG8000, 20mM sodium phophate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.52 Å R-free 0.165 |
| 3QTV Thrombin Inhibition by Pyridin Derivatives Deposited 2011-02-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 06P D-phenylalanyl-N-[(1-methylpyridinium-4-yl)methyl]-L-prolinamide × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.63 Å R-free 0.176 |
| 3QWC Thrombin Inhibition by Pyridin Derivatives Deposited 2011-02-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 GOL GLYCEROL × 1 98P D-phenylalanyl-N-[(4-chloro-1-methylpyridinium-3-yl)methyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.75 Å R-free 0.179 |
| 3QX5 Thrombin Inhibition by Pyridin Derivatives Deposited 2011-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 02P D-phenylalanyl-N-[(4-chloro-1-methylpyridinium-2-yl)methyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.35 Å R-free 0.156 |
| 3R3G Structure of human thrombin with residues 145-150 of murine thrombin. Deposited 2011-03-15 | Different construct Different mutation/modification 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
333–363（31 aa）
Fragment：UNP Residues 333-363
Chain B
364–622（259 aa）
Fragment：UNP Residues 364-622
|
Mutation：K508R, A513T, V515I, G516N, K517E, G518I | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1 M MES, pH 6.5 and 20% PEG20000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.75 Å R-free 0.222 |
| 3R3G Structure of human thrombin with residues 145-150 of murine thrombin. Deposited 2011-03-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
333–363（31 aa）
Fragment：UNP Residues 333-363
Chain B
364–622（259 aa）
Fragment：UNP Residues 364-622
|
Mutation：K508R, A513T, V515I, G516N, K517E, G518I | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NA SODIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1 M MES, pH 6.5 and 20% PEG20000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.75 Å R-free 0.222 |
| 3RLW Human Thrombin in complex with MI328 Deposited 2011-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 S28 N-(benzylsulfonyl)glycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 3 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG 8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.69 Å R-free 0.192 |
| 3RLY Human Thrombin in complex with MI329 Deposited 2011-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 S29 N-(benzylsulfonyl)-D-alanyl-N-(4-carbamimidoylbenzyl)-L-prolinamide × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG 8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.51 Å R-free 0.172 |
| 3RM0 Human Thrombin in complex with MI354 Deposited 2011-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 S54 N-(benzylsulfonyl)-D-valyl-N-(4-carbamimidoylbenzyl)-L-prolinamide × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG 8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.34 Å R-free 0.166 |
| 3RM2 Human Thrombin in complex with MI003 Deposited 2011-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 S00 N-(benzylsulfonyl)-3-cyclohexyl-D-alanyl-N-(4-carbamimidoylbenzyl)-L-prolinamide × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG 8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.23 Å R-free 0.163 |
| 3RML Human Thrombin in complex with MI331 Deposited 2011-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 M31 N-(benzylsulfonyl)glycyl-N-[2-(aminomethyl)-5-chlorobenzyl]-L-prolinamide × 1 GOL GLYCEROL × 2 PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG 8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.53 Å R-free 0.186 |
| 3RMM Human Thrombin in complex with MI332 Deposited 2011-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 M32 N-(benzylsulfonyl)-D-alanyl-N-[2-(aminomethyl)-5-chlorobenzyl]-L-prolinamide × 1 GOL GLYCEROL × 2 PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG 8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.58 Å R-free 0.179 |
| 3RMN Human Thrombin in complex with MI341 Deposited 2011-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 M41 N-(benzylsulfonyl)-D-valyl-N-[2-(aminomethyl)-5-chlorobenzyl]-L-prolinamide × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG 8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.78 Å R-free 0.185 |
| 3RMO Human Thrombin in complex with MI004 Deposited 2011-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 S04 N-(benzylsulfonyl)-3-cyclohexyl-D-alanyl-N-[2-(aminomethyl)-5-chlorobenzyl]-L-prolinamide × 1 GOL GLYCEROL × 2 PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG 8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.40 Å R-free 0.165 |
| 3S7H Structure of thrombin mutant Y225P in the E* form Deposited 2011-05-26 | Different construct Different mutation/modification 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
329–363（35 aa）
Fragment：Thrombin light chain
Chain B
364–622（259 aa）
Fragment：Thrombin heavy chain
|
Mutation：Y225P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；295 K；0.1 M Tris and 8% PEG 8000 , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.90 Å R-free 0.204 |
| 3S7K Structure of thrombin mutant Y225P in the E form Deposited 2011-05-26 | Different construct Different mutation/modification 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
329–363（35 aa）
Fragment：Thrombin light chain
Chain B
364–622（259 aa）
Fragment：Thrombin heavy chain
|
Mutation：Y225P | K POTASSIUM ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；295 K；0.2 M K Formate, 20 % PEG 3350, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.90 Å R-free 0.217 |
| 3S7K Structure of thrombin mutant Y225P in the E form Deposited 2011-05-26 | Different construct Different mutation/modification 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
329–363（35 aa）
Fragment：Thrombin light chain
Chain D
364–622（259 aa）
Fragment：Thrombin heavy chain
|
Mutation：Y225P | K POTASSIUM ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；295 K；0.2 M K Formate, 20 % PEG 3350, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.90 Å R-free 0.217 |
| 3SHA Human Thrombin In Complex With UBTHR97 Deposited 2011-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 P97 D-phenylalanyl-N-[(4-chloropyridin-3-yl)methyl]-L-prolinamide × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.52 Å R-free 0.190 |
| 3SHC Human Thrombin In Complex With UBTHR101 Deposited 2011-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 B01 D-phenylalanyl-N-[(4-chloropyridin-2-yl)methyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.90 Å R-free 0.197 |
| 3SI3 Human Thrombin In Complex With UBTHR103 Deposited 2011-06-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 GOL GLYCEROL × 1 PO4 PHOSPHATE ION × 1 B03 D-phenylalanyl-N-(pyridin-2-ylmethyl)-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.55 Å R-free 0.181 |
| 3SI4 Human Thrombin In Complex With UBTHR104 Deposited 2011-06-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 B04 D-phenylalanyl-N-[(1-methylpyridinium-2-yl)methyl]-L-prolinamide × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.27 Å R-free 0.159 |
| 3SQE Crystal structure of prethrombin-2 mutant S195A in the alternative form Deposited 2011-07-05 | 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 E
333–622（290 aa）
Fragment：unp residues 333-622
|
Mutation：S195A | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1 M Tris, 11% PEG8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.90 Å R-free 0.206 |
| 3SQH Crystal structure of prethrombin-2 mutant S195A in the the open form Deposited 2011-07-05 | 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 E
333–622（290 aa）
Fragment：unp residues 333-622
|
Mutation：S195A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1 M Tris, 11% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 8.5
|
Resolution 2.20 Å R-free 0.244 |
| 3SV2 Human Thrombin In Complex With UBTHR105 Deposited 2011-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 P05 D-phenylalanyl-N-(pyridin-4-ylmethyl)-L-prolinamide × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 3 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.30 Å R-free 0.165 |
| 3T5F Human Thrombin In Complex With MI340 Deposited 2011-07-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 M34 N-(benzylsulfonyl)-D-leucyl-N-[2-(aminomethyl)-5-chlorobenzyl]-L-prolinamide × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 3 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG 8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.45 Å R-free 0.172 |
| 3TU7 Human alpha-thrombin complexed with N-(methylsulfonyl)-D-phenylalanyl-N-((1-carbamimidoyl-4-piperidinyl)methyl)-l-prolinamide (BMS-189664) Deposited 2011-09-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：Thrombin heavy chain
Chain L
328–363（36 aa）
Fragment：Thrombin light chain
|
Not recorded | 0BM N-(methylsulfonyl)-D-phenylalanyl-N-[(1-carbamimidoylpiperidin-4-yl)methyl]-L-prolinamide × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.49 Å R-free 0.230 |
| 3U69 Unliganded wild-type human thrombin Deposited 2011-10-12 | Different construct Different mutation/modification 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
364–622（259 aa）
Fragment：unp residues 364-622
Chain L
334–363（30 aa）
Fragment：unp residues 334-363
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 BCN BICINE × 1 NA SODIUM ION × 1 IOD IODIDE ION × 1 CL CHLORIDE ION × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；50mM Tris, 50mM Bicine, 30mM NaF, 30mM NaBr, 30mM NaI, 11.5% MPD, 11.5% PEG 1000, 11.5% PEG 3350 , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.55 Å R-free 0.167 |
| 3U8O Human thrombin complexed with D-Phe-Pro-D-Arg-D-Thr Deposited 2011-10-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
334–363（30 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 IOD IODIDE ION × 1 CL CHLORIDE ION × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；293 K；50mM Tris, 50mM Bicine, 30mM NaF, 30mM NaBr, 30mM NaI, 11.5% MPD, 11.5% PEG-1000, 11.5% PEG-3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.28 Å R-free 0.149 |
| 3U8R Human thrombin complexed with D-Phe-Pro-D-Arg-Ile Deposited 2011-10-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
334–363（30 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 IOD IODIDE ION × 1 CL CHLORIDE ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；293 K；50mM Tris, 50mM Bicine, 30mM NaF, 30mM NaBr, 30mM NaI, 11.5% MPD, 11.5% PEG-1000, 11.5% PEG-3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.47 Å R-free 0.161 |
| 3U8T Human thrombin complexed with D-Phe-Pro-D-Arg-Cys Deposited 2011-10-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
334–360（27 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 IOD IODIDE ION × 1 CL CHLORIDE ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；50mM Tris, 50mM Bicine, 30mM NaF, 30mM NaBr, 30mM NaI, 11.5% MPD, 11.5% PEG-1000, 11.5% PEG-3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 8.5
|
Resolution 1.86 Å R-free 0.195 |
| 3U98 Human Thrombin In Complex With MI001 Deposited 2011-10-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 BJA (2S)-1-[(2R)-2-(benzylsulfonylamino)-5-guanidino-pentanoyl]-N-[(4-carbamimidoylphenyl)methyl]pyrrolidine-2-carboxamide × 1 PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.45 Å R-free 0.187 |
| 3U9A Human Thrombin In Complex With MI330 Deposited 2011-10-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 S33 (2S)-N-[[2-(aminomethyl)-5-chloranyl-phenyl]methyl]-1-[(2S)-2-[(3-chloranyl-4-methoxy-phenyl)sulfonylamino]-4-[(4-cyanophenyl)methylamino]-4-oxidanylidene-butanoyl]pyrrolidine-2-carboxamide × 1 GOL GLYCEROL × 2 PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.58 Å R-free 0.196 |
| 3UTU High affinity inhibitor of human thrombin Deposited 2011-11-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 |
| 3UWJ Human Thrombin In Complex With MI353 Deposited 2011-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 TIF N-(benzylsulfonyl)-D-leucyl-N-(4-carbamimidoylbenzyl)-L-prolinamide × 2 PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；15% PEG 8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 1.50 Å R-free 0.183 |
| 3VXE Human alpha-thrombin-Bivalirudin complex at PD5.0 Deposited 2012-09-12 | 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 H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；10% W/V PEG 4000, 100mm sodium acetate pD5.0 at room temperature, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.25 Å R-free 0.178 |
| 3VXF X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5 Deposited 2012-09-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
Experimental method not declared
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；THE CRYSTAL WAS OBTAINED BY A SITTING DROP VAPOR DIFFUSION AFTER MACROSEEDING. 2% (W/V) TO 10% (W/V) PEG4000, 100MM SODIUM ACETATE PD5.0. THE INITIAL CONCENTRATION OF THROMBIN-BIVALIRUDIN COMPLEX WAS 5MG/ML, pH 5.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution not provided |
| 4AX9 Human thrombin complexed with Napsagatran, RO0466240 Deposited 2012-06-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Fragment：THROMBIN HEAVY CHAIN, RESIDUES 364-620
Chain L
334–361（28 aa）
Fragment：THROMBIN LIGHT CHAIN, RESIDUES 334-361
|
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 |
| 4AYV Human thrombin - inhibitor complex Deposited 2012-06-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
332–361（30 aa）
Fragment：LIGHT CHAIN, RESIDUES 332-361
Chain B
364–620（257 aa）
Fragment：HEAVY CHAIN, RESIDUES 364-620
|
Not recorded | 9MQ {Benzyl-[(S)-3-[((S)-1-carbamimidoyl-piperidin-3-ylmethyl)-carbamoyl]-2-(naphthalene-2-sulfonylamino)-propionyl]-amino}-acetic acid × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.80 Å R-free 0.192 |
| 4AYY Human thrombin - inhibitor complex Deposited 2012-06-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
332–361（30 aa）
Fragment：LIGHT CHAIN, RESIDUES 332-361
Chain B
364–620（257 aa）
Fragment：HEAVY CHAIN, RESIDUES 364-620
|
Not recorded | 9MX (R)-1-[(S)-3-[((S)-1-Carbamimidoyl-piperidin-3-ylmethyl)-carbamoyl]-2-(naphthalene-2-sulfonylamino)-propionyl]-4-methyl-piperidine-2-carboxylic acid × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.60 Å R-free 0.197 |
| 4AZ2 Human thrombin - inhibitor complex Deposited 2012-06-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
332–361（30 aa）
Fragment：LIGHT CHAIN, RESIDUES 332-361
Chain B
364–620（257 aa）
Fragment：HEAVY CHAIN, RESIDUES 364-620
|
Not recorded | 9MU (R)-N-((S)-1-CARBAMIMIDOYL-PIPERIDIN-3-YLMETHYL)-2-(NAPHTHALENE-2-SULFONYLAMINO)-3-PHENYL-PROPIONAMIDE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.60 Å R-free 0.190 |
| 4BAH Thrombin in complex with inhibitor Deposited 2012-09-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | 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 |
| 4BAO Thrombin in complex with inhibitor Deposited 2012-09-14 | Different construct 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 A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | MVF (2S)-1-[(2R)-2-[(2-azanyl-2-oxidanylidene-ethyl)amino]-2-cyclohexyl-ethanoyl]-N-[(4-carbamimidoylphenyl)methyl]azetidine-2-carboxamide × 1 NA SODIUM ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.87 Å R-free 0.218 |
| 4BAQ Thrombin in complex with inhibitor Deposited 2012-09-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | 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 |
| 4BOH Madanins (MEROPS I53) are cleaved by thrombin and factor Xa Deposited 2013-05-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；0.1M TRIS-HCL PH 8.5, 0.2M LITHIUM SULFATE, 25% (W/V) PEG 3350
|
Resolution 2.60 Å R-free 0.239 |
| 4BOH Madanins (MEROPS I53) are cleaved by thrombin and factor Xa Deposited 2013-05-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
364–622（259 aa）
Chain B
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；0.1M TRIS-HCL PH 8.5, 0.2M LITHIUM SULFATE, 25% (W/V) PEG 3350
|
Resolution 2.60 Å R-free 0.239 |
| 4CH2 Low-salt crystal structure of a thrombin-GpIbalpha peptide complex Deposited 2013-11-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | GOL GLYCEROL × 2 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
pH 7.4；50 MM SODIUM FORMATE, 16% PEG-3350, pH 7.4
|
Resolution 1.60 Å R-free 0.187 |
| 4CH2 Low-salt crystal structure of a thrombin-GpIbalpha peptide complex Deposited 2013-11-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
328–363（36 aa）
Chain D
364–622（259 aa）
|
Not recorded | GOL GLYCEROL × 2 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
pH 7.4；50 MM SODIUM FORMATE, 16% PEG-3350, pH 7.4
|
Resolution 1.60 Å R-free 0.187 |
| 4CH8 High-salt crystal structure of a thrombin-GpIbalpha peptide complex Deposited 2013-11-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
Fragment：HEAVY CHAIN
|
Not recorded | NA SODIUM ION × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.4；100 MM SODIUM FORMATE, 18% PEG-3350, pH 7.4
|
Resolution 1.75 Å R-free 0.242 |
| 4CH8 High-salt crystal structure of a thrombin-GpIbalpha peptide complex Deposited 2013-11-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
328–363（36 aa）
Chain D
364–622（259 aa）
Fragment：HEAVY CHAIN
|
Not recorded | NA SODIUM ION × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.4；100 MM SODIUM FORMATE, 18% PEG-3350, pH 7.4
|
Resolution 1.75 Å R-free 0.242 |
| 4CH8 High-salt crystal structure of a thrombin-GpIbalpha peptide complex Deposited 2013-11-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
328–363（36 aa）
Chain F
364–622（259 aa）
Fragment：HEAVY CHAIN
|
Not recorded | NA SODIUM ION × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.4；100 MM SODIUM FORMATE, 18% PEG-3350, pH 7.4
|
Resolution 1.75 Å R-free 0.242 |
| 4CH8 High-salt crystal structure of a thrombin-GpIbalpha peptide complex Deposited 2013-11-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
328–363（36 aa）
Chain H
364–622（259 aa）
Fragment：HEAVY CHAIN
|
Not recorded | NA SODIUM ION × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.4；100 MM SODIUM FORMATE, 18% PEG-3350, pH 7.4
|
Resolution 1.75 Å R-free 0.242 |
| 4DIH X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of sodium ions Deposited 2012-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：Heavy chain fragment (UNP Residues 364-622)
Chain L
328–363（36 aa）
Fragment：Light chain fragment (UNP Residues 328-363)
|
Not recorded | ZN ZINC ION × 3 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 × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；10-15% w/v polyethylene glycol 8000, 0.05 M zinc acetate, 0.1 M sodium cacodylate
, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.80 Å R-free 0.213 |
| 4DII X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of potassium ions Deposited 2012-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：Heavy chain (UNP Residues 364-622)
Chain L
328–363（36 aa）
Fragment：Light chain (UNP Residues 328-363)
|
Not recorded | ZN ZINC ION × 2 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 CL CHLORIDE ION × 2 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；10-15% w/v polyethylene glycol 8000, 0.05 M zinc acetate, 0.1 M sodium cacodylate , pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.05 Å R-free 0.226 |
| 4DT7 Crystal structure of thrombin bound to the activation domain QEDQVDPRLIDGKMTRRGDS of protein C Deposited 2012-02-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
332–363（32 aa）
Chain B
364–622（259 aa）
|
Mutation：S195A | NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1 M Tris, pH 8.5, 0.2 M Na acetate, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.90 Å R-free 0.218 |
| 4DT7 Crystal structure of thrombin bound to the activation domain QEDQVDPRLIDGKMTRRGDS of protein C Deposited 2012-02-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
332–363（32 aa）
Chain D
364–622（259 aa）
|
Mutation：S195A | NA SODIUM ION × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1 M Tris, pH 8.5, 0.2 M Na acetate, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.90 Å R-free 0.218 |
| 4DY7 Crystal structures of protease nexin-1 in complex with S195A thrombin Deposited 2012-02-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
315–363（49 aa）
Fragment：UNP residues 315-363
Chain B
364–622（259 aa）
|
Mutation：S195A | ACT ACETATE ION × 3 CA CALCIUM ION × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.4；295 K；0.14M calcium acetate, 13% PEG3350, pH 7.4, VAPOR DIFFUSION, temperature 295K
|
Resolution 2.80 Å R-free 0.268 |
| 4DY7 Crystal structures of protease nexin-1 in complex with S195A thrombin Deposited 2012-02-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
315–363（49 aa）
Fragment：UNP residues 315-363
Chain E
364–622（259 aa）
|
Mutation：S195A | CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.4；295 K；0.14M calcium acetate, 13% PEG3350, pH 7.4, VAPOR DIFFUSION, temperature 295K
|
Resolution 2.80 Å R-free 0.268 |
| 4E05 Anophelin from the malaria vector inhibits thrombin through a novel reverse-binding mechanism Deposited 2012-03-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：heavy chain (UNP residues 364-622)
Chain L
328–363（36 aa）
Fragment：light chain (UNP residues 328-363)
|
Not recorded | 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 7.5；293 K；100 mM HEPES, pH 7.5, 1.4 M tri-sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.30 Å R-free 0.201 |
| 4E06 Anophelin from the malaria vector inhibits thrombin through a novel reverse-binding mechanism Deposited 2012-03-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：heavy chain (UNP residues 364-622)
Chain L
328–363（36 aa）
Fragment：light chain (UNP residues 328-363)
|
Not recorded | 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 4.5；293 K；100 mM sodium acetate, pH 4.5, 3 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 3.20 Å R-free 0.208 |
| 4E7R Thrombin in complex with 3-amidinophenylalanine inhibitor Deposited 2012-03-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0NW 3-[(2S)-3-[4-(2-aminoethyl)piperidin-1-yl]-2-{[(2',4'-dichlorobiphenyl-3-yl)sulfonyl]amino}-3-oxopropyl]benzenecarboximidamide × 1 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；277.15 K；15% PEG8000, 20MM SODIUM PHOSPHATE, 175MM SODIUM CHLORIDE, PH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 2.25 Å R-free 0.223 |
| 4E7R Thrombin in complex with 3-amidinophenylalanine inhibitor Deposited 2012-03-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
364–622（259 aa）
Chain M
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0NW 3-[(2S)-3-[4-(2-aminoethyl)piperidin-1-yl]-2-{[(2',4'-dichlorobiphenyl-3-yl)sulfonyl]amino}-3-oxopropyl]benzenecarboximidamide × 1 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；277.15 K；15% PEG8000, 20MM SODIUM PHOSPHATE, 175MM SODIUM CHLORIDE, PH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
|
Resolution 2.25 Å R-free 0.223 |
| 4H6S Crystal structure of thrombin mutant E14eA/D14lA/E18A/S195A Deposited 2012-09-19 | Different construct Different mutation/modification 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
333–363（31 aa）
Chain B
364–622（259 aa）
|
Mutation：E14eA,D14lA,E18A,S195A | NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；295 K；0.2M NH4Cl and 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.19 Å R-free 0.259 |
| 4H6T Crystal structure of prethrombin-2 mutant E14eA/D14lA/E18A/S195A Deposited 2012-09-19 | 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
317–622（306 aa）
|
Mutation：E14eA,D14lA,E18A,S195A | PO4 PHOSPHATE ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.7；295 K；0.2M KH2PO4 and 20% PEG 3350, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.40 Å R-free 0.253 |
| 4HFP Structure of thrombin mutant S195a bound to the active site inhibitor argatroban Deposited 2012-10-05 | Different construct Different mutation/modification 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
333–363（31 aa）
Chain B
364–622（259 aa）
|
Mutation：S195A | NA SODIUM ION × 1 15U (2R,4R)-4-methyl-1-(N~2~-{[(3S)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonyl}-L-arginyl)piperidine-2-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；100mM Na acetate pH 4.6 and 25% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.40 Å R-free 0.238 |
| 4HFP Structure of thrombin mutant S195a bound to the active site inhibitor argatroban Deposited 2012-10-05 | Different construct Different mutation/modification 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
333–363（31 aa）
Chain D
364–622（259 aa）
|
Mutation：S195A | NA SODIUM ION × 1 15U (2R,4R)-4-methyl-1-(N~2~-{[(3S)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonyl}-L-arginyl)piperidine-2-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；100mM Na acetate pH 4.6 and 25% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.40 Å R-free 0.238 |
| 4HTC THE REFINED STRUCTURE OF THE HIRUDIN-THROMBIN COMPLEX Deposited 1993-06-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å |
| 4HTC THE REFINED STRUCTURE OF THE HIRUDIN-THROMBIN COMPLEX Deposited 1993-06-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å |
| 4HZH Structure of recombinant Gla-domainless prothrombin mutant S525A Deposited 2012-11-15 | 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
90–622（533 aa）
Fragment：UNP residues 90-622
|
Mutation：S525A | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；100 mM Tris-Hcl, pH 8.5 and 25% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.30 Å R-free 0.329 |
| 4HZH Structure of recombinant Gla-domainless prothrombin mutant S525A Deposited 2012-11-15 | 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 B
90–622（533 aa）
Fragment：UNP residues 90-622
|
Mutation：S525A | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；100 mM Tris-Hcl, pH 8.5 and 25% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 3.30 Å R-free 0.329 |
| 4I7Y Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II Deposited 2012-12-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：HEAVY CHAIN (UNP Residues 364-622)
Chain L
328–363（36 aa）
Fragment：LIGHT CHAIN (UNP Residues 328-363)
|
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 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；14% PEG 3350, 0.2 M sodium citrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.40 Å R-free 0.249 |
| 4LOY Crystal Structure Analysis of thrombin in complex with compound D57, 5-Chlorothiophene-2-carboxylic acid [(S)-2-[2-methyl-3-(2- oxopyrrolidin-1-yl)benzenesulfonylamino]-3-(4-methylpiperazin-1- yl)-3-oxopropyl]amide (SAR107375) Deposited 2013-07-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–620（257 aa）
Fragment：unp residues 364-620
Chain L
334–360（27 aa）
Fragment：unp residues 334-360
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 6XS 5-Chloro-thiophene-2-carboxylic acid [(S)-2-[2-chloro-5-fluoro-3-(2-oxo-piperidin-1-yl)-benzenesulfonylamino]-3-(4-methyl-piperazin-1-yl)-3-oxo-propyl]-amide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.2；278 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 278K
|
Resolution 1.77 Å R-free 0.208 |
| 4LXB Crystal Structure Analysis of thrombin in complex with compound D58 Deposited 2013-07-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 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 |
| 4LZ1 X-ray structure of the complex between human thrombin and the TBA deletion mutant lacking thymine 12 nucleobase Deposited 2013-07-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 K POTASSIUM ION × 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 5.8；293 K；PEG 3350 25%, 0.2 M ammonium acetate, 0.1 M Bis/Tris, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.65 Å R-free 0.190 |
| 4LZ4 X-ray structure of the complex between human thrombin and the TBA deletion mutant lacking thymine 3 nucleobase Deposited 2013-07-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 NA SODIUM ION × 1 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；60% Tacsimate, 1-3% MPEG 5K or PEG 8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.56 Å R-free 0.227 |
| 4LZ4 X-ray structure of the complex between human thrombin and the TBA deletion mutant lacking thymine 3 nucleobase Deposited 2013-07-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain C
328–363（36 aa）
Chain D
364–622（259 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 NA SODIUM ION × 1 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；60% Tacsimate, 1-3% MPEG 5K or PEG 8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.56 Å R-free 0.227 |
| 4MLF Crystal structure for the complex of thrombin mutant D102N and hirudin Deposited 2013-09-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–363（33 aa）
Fragment：Thrombin light chain (UNP residues 331-363)
Chain B
364–622（259 aa）
Fragment：Thrombin heavy chain (UNP residues 364-622)
|
Mutation：D102N | 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 |
| 4NZQ Crystal structure of Ca2+-free prothrombin deletion mutant residues 146-167 Deposited 2013-12-12 | 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）
Chain A
211–622（412 aa）
|
Mutation：deletion mutant residues 146-167 Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：deletion mutant residues 146-167 Non-standard monomer：Yes (specific site not provided by mmCIF) | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100 mM Tris-HCl, pH 8.5 and 30% PEG300, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.81 Å R-free 0.279 |
| 4O03 Crystal structure of Ca2+ bound prothrombin deletion mutant residues 146-167 Deposited 2013-12-13 | 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）
Chain A
211–622（412 aa）
|
Mutation：deletion mutant residues 146-167 Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：deletion mutant residues 146-167 Non-standard monomer：Yes (specific site not provided by mmCIF) | CA CALCIUM ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM HEPES, pH 7.5, 10% PEG 4000 and 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.38 Å R-free 0.279 |
| 4RKJ Crystal structure of thrombin mutant S195T (free form) Deposited 2014-10-13 | Different construct Different mutation/modification 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
330–363（34 aa）
Chain B
364–622（259 aa）
|
Mutation：S195T | K POTASSIUM ION × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；0.2 M K formate and 21% PEG3350, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.207 |
| 4RKO Crystal structure of thrombin mutant S195T bound with PPACK Deposited 2014-10-13 | Different construct Different mutation/modification 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
322–363（42 aa）
Chain B
364–622（259 aa）
|
Mutation：S195T | 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 GOL GLYCEROL × 2 NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M MES, pH 6.5, 15% PEG 6000 and 5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.84 Å R-free 0.202 |
| 4RN6 Structure of prethrombin-2 mutant s195a bound to the active site inhibitor argatroban Deposited 2014-10-23 | 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
333–622（290 aa）
Fragment：UNP residues 333-622
|
Mutation：S195A | 15U (2R,4R)-4-methyl-1-(N~2~-{[(3S)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonyl}-L-arginyl)piperidine-2-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；100 mM TRIS PH 8.5, 200 mM LI2SO4 AND 30% PEG 3000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K
|
Resolution 3.00 Å R-free 0.343 |
| 4RN6 Structure of prethrombin-2 mutant s195a bound to the active site inhibitor argatroban Deposited 2014-10-23 | 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 B
333–622（290 aa）
Fragment：UNP residues 333-622
|
Mutation：S195A | 15U (2R,4R)-4-methyl-1-(N~2~-{[(3S)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonyl}-L-arginyl)piperidine-2-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；100 mM TRIS PH 8.5, 200 mM LI2SO4 AND 30% PEG 3000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K
|
Resolution 3.00 Å R-free 0.343 |
| 4THN THE CRYSTAL STRUCTURE OF ALPHA-THROMBIN-HIRUNORM IV COMPLEX REVEALS A NOVEL SPECIFICITY SITE RECOGNITION MODE. Deposited 1998-09-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；pH 7.0
|
Resolution 2.50 Å |
| 4UD9 Thrombin in complex with 5-chlorothiophene-2-carboxamide Deposited 2014-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：THROMBIN HEAVY CHAIN, UNP RESIDUES 364-622
Chain L
333–360（28 aa）
Fragment：THROMBIN LIGHT CHAIN, UNP RESIDUES 333-360
|
Not recorded | NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 DMS DIMETHYL SULFOXIDE × 2 GOL GLYCEROL × 3 EDO 1,2-ETHANEDIOL × 2 FQI 5-CHLORO-2-THIOPHENECARBOXAMIDE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
|
Resolution 1.12 Å R-free 0.141 |
| 4UDW Thrombin in complex with 1-(2R)-2-amino-3-phenyl-propanoyl-N-(2, 5dichlorophenyl)methylpyrrolidine-2-carboxamide Deposited 2014-12-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Fragment：THROMBIN HEAVY CHAIN, UNP RESIDUES 364-620
Chain L
333–360（28 aa）
Fragment：THROMBIN LIGHT CHAIN, UNP RESIDUES 333-360
|
Not recorded | NA SODIUM ION × 2 N6L D-phenylalanyl-N-(2,5-dichlorobenzyl)-L-prolinamide × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
|
Resolution 1.16 Å R-free 0.141 |
| 4UE7 Thrombin in complex with 1-amidinopiperidine Deposited 2014-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Fragment：THROMBIN HEAVY CHAIN, UNP RESIDUES 364-621
Chain L
333–360（28 aa）
Fragment：THROMBIN LIGHT CHAIN, UNP RESIDUES 333-360
|
Not recorded | IOD IODIDE ION × 1 GOL GLYCEROL × 3 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 DMS DIMETHYL SULFOXIDE × 3 EDO 1,2-ETHANEDIOL × 1 MRZ piperidine-1-carboximidamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
|
Resolution 1.13 Å R-free 0.139 |
| 4UEH Thrombin in complex with benzamidine Deposited 2014-12-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Fragment：THROMBIN HEAVY CHAIN, UNP RESIDUES 364-621
Chain L
333–361（29 aa）
Fragment：THROMBIN LIGHT CHAIN, UNP RESIDUES 333-361
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 BEN BENZAMIDINE × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
|
Resolution 1.16 Å R-free 0.138 |
| 4UFD Thrombin in complex with 4-(((1-((2S)-1-((2R)-2-(benzylsulfonylamino)- 3-phenyl-propanoyl)pyrrolidin-2-yl)-1-oxo-ethyl)amino)methyl) benzamidine Deposited 2015-03-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Fragment：RESIDUES 364-621
Chain L
333–361（29 aa）
Fragment：RESIDUES 333-361
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 GOL GLYCEROL × 2 S49 (2S)-N-[(4-carbamimidoylphenyl)methyl]-1-[(2R)-3-phenyl-2-[(phenylmethyl)sulfonylamino]propanoyl]pyrrolidine-2-carboxamide × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
|
Resolution 1.43 Å R-free 0.159 |
| 4UFE Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4- carbamimidoylphenyl)methylamino)-2-oxo-butyl)-3-phenyl-propanamide Deposited 2015-03-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Fragment：RESIDUES 364-621
Chain L
333–361（29 aa）
Fragment：RESIDUES 333-361
|
Not recorded | NA SODIUM ION × 2 3ZD (2R)-N-[(2S)-1-[(4-carbamimidoylphenyl)methylamino]-1-oxidanylidene-propan-2-yl]-3-phenyl-2-[(phenylmethyl)sulfonylamino]propanamide × 1 PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；SEE MATERIALS AND METHODS SECTION OF PUBLICATION, PH 7.5
|
Resolution 1.59 Å R-free 0.182 |
| 4UFF Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4- carbamimidoylphenyl)methylamino)-2-oxo-ethyl)-N-methyl-3-phenyl- propanamide Deposited 2015-03-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Fragment：RESIDUES 364-621
Chain L
333–361（29 aa）
Fragment：RESIDUES 333-361
|
Not recorded | NA SODIUM ION × 2 6V2 (2R)-2-(benzylsulfonylamino)-N-(2-((4-carbamimidoylphenyl)methylamino)-2-oxo-ethyl)-N-methyl-3-phenyl-propanamide × 1 PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
|
Resolution 1.55 Å R-free 0.187 |
| 4UFG Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-((1S)-2-((4- carbamimidoylphenyl)methylamino)-1-methyl-2-oxo-ethyl)-N-methyl-3- phenyl-propanamide ethane Deposited 2015-03-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Fragment：RESIDUES 364-621
Chain L
333–361（29 aa）
Fragment：RESIDUES 333-361
|
Not recorded | NA SODIUM ION × 2 D6J (2S)-N-[(4-carbamimidoylphenyl)methyl]-2-[methyl-[(2R)-3-phenyl-2-[(phenylmethyl)sulfonylamino]propanoyl]amino]butanamide × 1 PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
|
Resolution 1.65 Å R-free 0.186 |
| 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | 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 |
| 5A2M Thrombin Inhibitor Deposited 2015-05-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Fragment：THROMBIN HEAVY CHAIN, UNP RESIDUES 364-621
Chain L
333–361（29 aa）
Fragment：THROMBIN LIGHT CHAIN, UNP RESIDUES 333-361
|
Not recorded | GOL GLYCEROL × 1 NA SODIUM ION × 2 WX5 (2S)-1-[(2R)-5-carbamimidamido-2-[(phenylmethyl)sulfonylamino]pentanoyl]-N-[[5-chloranyl-2-(hydroxymethyl)phenyl]methyl]pyrrolidine-2-carboxamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；SEE MATERIALS&METHODS OF PUBLICATION, pH 7.5
|
Resolution 1.40 Å R-free 0.159 |
| 5AF9 Thrombin in complex with 4-Methoxy-N-(2-pyridinyl)benzamide Deposited 2015-01-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Fragment：THROMBIN HEAVY CHAIN, UNP RESIDUES 364-621
Chain L
333–361（29 aa）
Fragment：THROMBIN LIGHT CHAIN, UNP RESIDUES 333-361
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 DMS DIMETHYL SULFOXIDE × 2 SJR 4-methoxy-N-(pyridin-2-yl)benzamide × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 3 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
|
Resolution 1.18 Å R-free 0.137 |
| 5AFY Thrombin in complex with 3-chloro-benzamide Deposited 2015-01-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Fragment：RESIDUES 364-621
Chain L
333–361（29 aa）
Fragment：RESIDUES 333-361
|
Not recorded | NA SODIUM ION × 2 WCE 3-CHLORO-BENZAMIDE × 1 DMS DIMETHYL SULFOXIDE × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
|
Resolution 1.12 Å R-free 0.138 |
| 5AFZ Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4- carbamimidoylphenyl)methylamino)-2-oxo-propyl)-3-phenyl-propanamide Deposited 2015-01-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Fragment：RESIDUES 364-621
Chain L
333–361（29 aa）
Fragment：RESIDUES 333-361
|
Not recorded | NA SODIUM ION × 2 UET N-(BENZYLSULFONYL)-D-PHENYLALANYL-N-(4-CARBAMIMIDOYLBENZYL)GLYCINAMIDE × 1 PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
|
Resolution 1.53 Å R-free 0.174 |
| 5AHG Thrombin in complex with ((4-chlorophenyl)sulfamoyl))diemethylamine Deposited 2015-02-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Fragment：RESIDUES 364-621
Chain L
333–361（29 aa）
Fragment：RESIDUES 333-361
|
Not recorded | NA SODIUM ION × 2 DMS DIMETHYL SULFOXIDE × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 Y4L ((4-Chlorophenyl)sulfamoyl))dimethylamine × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；SEE MATERIAL AND METHODS SECTION OF PUBLICATION, pH 7.5
|
Resolution 1.24 Å R-free 0.144 |
| 5CMX X-ray structure of the complex between human alpha thrombin and a duplex/quadruplex 31-mer DNA aptamer Deposited 2015-07-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.2 M sodium malonate pH 7, 18 % PEG 3350
|
Resolution 2.98 Å R-free 0.231 |
| 5DO4 Thrombin-RNA aptamer complex Deposited 2015-09-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Chain L
328–363（36 aa）
|
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 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 2 CA CALCIUM ION × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；5% [w/v] PEG-6000, 2.5% v/v (+/-)-2-Methyl-2,4-pentanediol, 50 mM HEPES
|
Resolution 1.86 Å R-free 0.224 |
| 5E8E Crystal structure of thrombin bound to an exosite 1-specific IgA Fab Deposited 2015-10-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
Fragment：COAGULATION FACTOR II
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 3 PO4 PHOSPHATE ION × 5 CIT CITRIC ACID × 1 NA SODIUM ION × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 4.2；298 K；100MM SODIUM PHOSPHATE/CITRATE, PH 4.2, 40% PEG300
|
Resolution 1.90 Å R-free 0.244 |
| 5EDK Crystal structure of prothrombin deletion mutant residues 146-167 ( Form II ). Deposited 2015-10-21 | 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
44–622（579 aa）
|
Mutation：Deletion mutant residues 146-167 Non-standard monomer：Yes (specific site not provided by mmCIF) | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9.1；293 K；0.2 M di-Na hydrogen phosphate and 20% PEG 3350
|
Resolution 3.21 Å R-free 0.323 |
| 5EDM Crystal structure of prothrombin deletion mutant residues 154-167 ( Form I ) Deposited 2015-10-21 | 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
44–622（579 aa）
|
Mutation：deletion mutant residues 154-167 Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 9 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M MES, pH 6.5 and 1.6 M MgSO4
|
Resolution 2.20 Å R-free 0.236 |
| 5EW1 Human thrombin sandwiched between two DNA aptamers: HD22 and HD1-deltaT3 Deposited 2015-11-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；28% MPEG 2000,
0.1 M Bis/Tris pH 6.5
|
Resolution 2.95 Å R-free 0.208 |
| 5EW2 Human thrombin sandwiched between two DNA aptamers: HD22 and HD1-deltaT12 Deposited 2015-11-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；18% PEG 3350, 0.2 M Sodium Formate, 2% acetonitrile
|
Resolution 3.59 Å R-free 0.268 |
| 5GDS HIRUNORMS ARE TRUE HIRUDIN MIMETICS. THE CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN:HIRUNORM V COMPLEX Deposited 1997-07-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；277 K；THE CRYSTALS OF THROMBIN:HIRUNORM V COMPLEX WERE GROWN, AS DESCRIBED BY SKRZYPEZAK ET AL. (1991) J. MOL. BIOL.,221,1379-1393 BY VAPOR DIFFUSION METHODS AT 4 C. A 6 MICROLITER DROP, CONTAINING 0.05 M SODIUM HEPES (PH 7.0) 10% (W/V) PEG 4000 0.02% NAN3, 20 MG/ML. THROMBIN:HIRUNORM V COMPLEX WAS EQUILIBRATED AGAINST A PRECIPITATING SOLUTION CONTAINING 0.1 M SODIUM HEPES (PH 7.0) 20% (W/V) PEG 4000 0.04% NAN3. CRYSTAL OF THROMBIN:HIRUGEN COMPLEX WERE CRUSHED AND INDIVIDUAL SEEDS WERE USED FOR CROSS-SEEDING EXPERIMENTS., vapor diffusion, temperature 277K
|
Resolution 2.10 Å |
| 5GIM Crystal structure of thrombin-avathrin complex Deposited 2016-06-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
328–363（36 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；0.1M HEPES, 20-25% PEG 8000
|
Resolution 2.09 Å R-free 0.216 |
| 5JDU Crystal structure for human thrombin mutant D189A Deposited 2016-04-17 | Different construct Different mutation/modification 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
331–363（33 aa）
Chain B
364–622（259 aa）
|
Mutation：D189A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.9；295 K；200 mM KCl and 20% PEG 3350
|
Resolution 1.70 Å R-free 0.206 |
| 5JDU Crystal structure for human thrombin mutant D189A Deposited 2016-04-17 | Different construct Different mutation/modification 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
331–363（33 aa）
Chain D
364–622（259 aa）
|
Mutation：D189A | CL CHLORIDE ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.9；295 K；200 mM KCl and 20% PEG 3350
|
Resolution 1.70 Å R-free 0.206 |
| 5JFD Thrombin in complex with (S)-N-(2-(aminomethyl)-5-chlorobenzyl)-1-((benzylsulfonyl)-D-arginyl)pyrrolidine-2-carboxamide Deposited 2016-04-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 2TS (2S)-N-[[2-(aminomethyl)-5-chloro-phenyl]methyl]-1-[(2R)-5-carbamimidamido-2-(phenylmethylsulfonylamino)pentanoyl]pyrrolidine-2-carboxamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 GOL GLYCEROL × 2 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20 mM Sodium dihydrogen phosphate ph 7.5,
350 mM NACl, 27% PEG 8000,
|
Resolution 1.46 Å R-free 0.163 |
| 5JZY Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide Deposited 2016-05-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 DMS DIMETHYL SULFOXIDE × 3 PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 6OV 3-cyclohexyl-D-alanyl-N-[(4-carbamimidoylphenyl)methyl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20 mM Sodium dihydrogen phosphate ph 7.5,
350 mM NaCl,
27% PEG 8000
|
Resolution 1.27 Å R-free 0.142 |
| 5L6N Disulfated madanin-thrombin complex Deposited 2016-05-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 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, SITTING DROP；293 K；0.1 M MMT buffer pH 7.0, 30% (w/v) PEG 1500
|
Resolution 1.63 Å R-free 0.199 |
| 5LCE Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N-(5-chloro-2-(hydroxymethyl)benzy l)pyrrolidine-2-carboxamide Deposited 2016-06-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 6TH (2~{S})-1-[(2~{R})-2-azanyl-3-cyclohexyl-propanoyl]-~{N}-[[5-chloranyl-2-(hydroxymethyl)phenyl]methyl]pyrrolidine-2-carboxamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 1 DMS DIMETHYL SULFOXIDE × 1 NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20 mM Sodium dihydrogen phosphate ph 7.5,
350 mM NaCl
27% PEG 8000
|
Resolution 1.39 Å R-free 0.168 |
| 5LPD Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N-(2-(aminomethyl)-5-chlorobenzyl) pyrrolidine-2-carboxamide Deposited 2016-08-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 DMS DIMETHYL SULFOXIDE × 1 71U (2~{S})-~{N}-[[2-(aminomethyl)-5-chloranyl-phenyl]methyl]-1-[(2~{R})-2-azanyl-3-cyclohexyl-propanoyl]pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20 mM Sodium dihydrogen phosphate ph 7.5, 350 mM NaCl, 27% PEG 8000
|
Resolution 1.50 Å R-free 0.170 |
| 5MJT Thrombin Mutant A190S in complex with (S) -1 - ((R) -2-amino-3,3-diphenylpropanoyl) -N- (3-chlorobenzyl) pyrrolidine-2-carboxamide Deposited 2016-12-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 23U beta-phenyl-D-phenylalanyl-N-(3-chlorobenzyl)-L-prolinamide × 1 DMS DIMETHYL SULFOXIDE × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 5 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20 mM Sodium dihydrogen phosphate ph 7.5, 350 mM NaCl, 27% PEG 8000
|
Resolution 1.40 Å R-free 0.172 |
| 5MLS Thrombin Mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(3-chlorobenzyl)pyrrolidine-2-carboxamide Deposited 2016-12-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | 22U D-phenylalanyl-N-(3-chlorobenzyl)-L-prolinamide × 1 DMS DIMETHYL SULFOXIDE × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 6 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20 mM Sodium dihydrogen phosphate ph 7.5, 350 mM NaCl, 27% PEG 8000
|
Resolution 1.62 Å R-free 0.180 |
| 5MM6 Thrombin Mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide Deposited 2016-12-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | GOL GLYCEROL × 5 DMS DIMETHYL SULFOXIDE × 2 PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 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；20 mM sodium dihydrogen phosphate ph 7.5, 350 mM NaCl, 27% PEG 8000
|
Resolution 1.29 Å R-free 0.142 |
| 5NHU HUMAN ALPHA THROMBIN COMPLEXED WITH ANOPHELES GAMBIAE cE5 ANTICOAGULANT Deposited 2017-03-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 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, SITTING DROP；pH 5；293 K；Drops consisting of equal volumes (1 microliter) of protein complex (at 6.4 mg/mL) and precipitant solution (0.1M PCTP pH 5.0, 25% w/v PEG 1500) equilibrated against a 300 microliter reservoir.
|
Resolution 1.45 Å R-free 0.203 |
| 5NHU HUMAN ALPHA THROMBIN COMPLEXED WITH ANOPHELES GAMBIAE cE5 ANTICOAGULANT Deposited 2017-03-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
364–622（259 aa）
Chain B
328–363（36 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, SITTING DROP；pH 5；293 K；Drops consisting of equal volumes (1 microliter) of protein complex (at 6.4 mg/mL) and precipitant solution (0.1M PCTP pH 5.0, 25% w/v PEG 1500) equilibrated against a 300 microliter reservoir.
|
Resolution 1.45 Å R-free 0.203 |
| 5NHU HUMAN ALPHA THROMBIN COMPLEXED WITH ANOPHELES GAMBIAE cE5 ANTICOAGULANT Deposited 2017-03-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
364–622（259 aa）
Chain D
328–363（36 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, SITTING DROP；pH 5；293 K；Drops consisting of equal volumes (1 microliter) of protein complex (at 6.4 mg/mL) and precipitant solution (0.1M PCTP pH 5.0, 25% w/v PEG 1500) equilibrated against a 300 microliter reservoir.
|
Resolution 1.45 Å R-free 0.203 |
| 5TO3 Crystal structure of thrombin mutant W215A/E217A fused to EGF456 of thrombomodulin via a 31-residue linker and bound to PPACK Deposited 2016-10-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
318–363（46 aa）
Chain B
364–621（258 aa）
|
Mutation：W215A, E217A | 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 K POTASSIUM ION × 1 NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；100 mM HEPES and 20% PEG 8000
|
Resolution 2.34 Å R-free 0.255 |
| 5Z5W VFR12 in complex with LPS micelles Deposited 2018-01-21 | Different construct 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
606–617（12 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 4.5；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition
0.5 mM Thrombin C-terminal Peptide, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 5Z5X HVF18 in complex with LPS micelles Deposited 2018-01-21 | Different construct 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
605–622（18 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 4.5；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition
0.5 mM HVF18, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 6BJR Crystal structure of prothrombin mutant S101C/A470C Deposited 2017-11-06 | 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
44–622（579 aa）
|
Mutation：S101C, A470C Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；277 K；100 mM Bicine, pH 8.5 and 16% PEG3350
|
Resolution 6.00 Å R-free 0.293 |
| 6C2W Crystal structure of human prothrombin mutant S101C/A470C Deposited 2018-01-09 | 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
44–622（579 aa）
|
Mutation：S101C, A470C Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 9；277 K；100 mM Bicine, pH 9.0 and 11% PEG 3350
|
Resolution 4.12 Å R-free 0.333 |
| 6C2W Crystal structure of human prothrombin mutant S101C/A470C Deposited 2018-01-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
44–622（579 aa）
|
Mutation：S101C, A470C Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 9；277 K；100 mM Bicine, pH 9.0 and 11% PEG 3350
|
Resolution 4.12 Å R-free 0.333 |
| 6CYM Reversible Covalent Direct Thrombin Inhibitors Deposited 2018-04-06 | Different construct Different mutation/modification 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
364–622（259 aa）
Chain B
334–361（28 aa）
|
Not recorded | 71F 2-methoxybenzoic acid × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；294 K；For complex formation, 2 mg human alpha-thrombin (7.1 mg/mL in 50% v/v glycerol) were mixed with 0.5 mM Compound 1 in DMSO and dialyzed overnight into a solution of 20 mM sodium citrate and 1.3 mM Na2SO4 (pH 5.8). After dialysis, another 0.5 mM compound were added and left to incubate at room temperature for 1 h. The protein was centrifuged for 5 min at 4 deg C and 8000x RCF. The pellet, including about 120 uL of buffer, was mixed with 100 uL of a solution containing 50 mM sodium phosphate (pH 7.3), 190 mM sodium chloride, and 0.2 mM Compound 1. The crystal used for data collection was grown from the JCSG+ screen in well A10. The crystal was grown at 20 deg C using a MRC 3-well plate and in a 150 + 150 nL drop with a reservoir of 0.2 M potassium formate and 20% w/v PEG-3350.
|
Resolution 2.90 Å R-free 0.254 |
| 6CYM Reversible Covalent Direct Thrombin Inhibitors Deposited 2018-04-06 | Different construct Different mutation/modification 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
364–622（259 aa）
Chain D
334–361（28 aa）
|
Not recorded | 71F 2-methoxybenzoic acid × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；294 K；For complex formation, 2 mg human alpha-thrombin (7.1 mg/mL in 50% v/v glycerol) were mixed with 0.5 mM Compound 1 in DMSO and dialyzed overnight into a solution of 20 mM sodium citrate and 1.3 mM Na2SO4 (pH 5.8). After dialysis, another 0.5 mM compound were added and left to incubate at room temperature for 1 h. The protein was centrifuged for 5 min at 4 deg C and 8000x RCF. The pellet, including about 120 uL of buffer, was mixed with 100 uL of a solution containing 50 mM sodium phosphate (pH 7.3), 190 mM sodium chloride, and 0.2 mM Compound 1. The crystal used for data collection was grown from the JCSG+ screen in well A10. The crystal was grown at 20 deg C using a MRC 3-well plate and in a 150 + 150 nL drop with a reservoir of 0.2 M potassium formate and 20% w/v PEG-3350.
|
Resolution 2.90 Å R-free 0.254 |
| 6EO6 X-ray structure of the complex between human alpha-thrombin and modified 15-mer DNA aptamer containing 5-(3-(2-(1H-indol-3-yl)acetamide-N-yl)-1-propen-1-yl)-2'-deoxyuridine residue Deposited 2017-10-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | K POTASSIUM ION × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；281 K；18% W/V PEG4000, 20% V/V 2-PROPANOL,
0.2 M SODIUM CITRATE
|
Resolution 1.69 Å R-free 0.168 |
| 6EO7 X-ray structure of the complex between human alpha-thrombin and modified 15-mer DNA aptamer containing 5-(3-(acetamide-N-yl)-1-propen-1-yl)-2'-deoxyuridine residue Deposited 2017-10-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | K POTASSIUM ION × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；281 K；25% W/V PEG4000, 24% V/V 2-PROPANOL,
0.2 M SODIUM CITRATE
|
Resolution 2.24 Å R-free 0.208 |
| 6EO8 Crystal structure of thrombin in complex with a novel glucose-conjugated potent inhibitor Deposited 2017-10-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 6 2FN N-(2-{[5-(5-chlorothiophen-2-yl)-1,2-oxazol-3-yl]methoxy}-6-[3-(beta-D-glucopyranosyloxy)propoxy]phenyl)-1-(propan-2-yl)piperidine-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG 4000, 0.1M HEPES pH7.0, 0.75M NaCl, 0.04% NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.94 Å R-free 0.248 |
| 6EO9 Crystal structure of thrombin in complex with a novel glucose-conjugated potent inhibitor Deposited 2017-10-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 6 2OJ N-(2-{[5-(5-chlorothiophen-2-yl)-1,2-oxazol-3-yl]methoxy}-6-{3-[(2,3,4,6-tetra-O-acetyl-beta-D-glucopyranosyl)oxy]propoxy}phenyl)-1-(propan-2-yl)piperidine-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG 4000, 0.1M HEPES pH7.0, 0.75M NaCl, 0.04% NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K, temperature 293K
|
Resolution 1.84 Å R-free 0.248 |
| 6EVV X-ray structure of the complex between human alpha thrombin and NU172, a duplex/quadruplex 26-mer DNA aptamer, in the presence of potassium ions. Deposited 2017-11-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–360（33 aa）
|
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 K POTASSIUM ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Tacsimate 50 % v/v, pH 7.0
|
Resolution 2.50 Å R-free 0.205 |
| 6FJT 4-chloro-benzamidine in complex with thrombin Deposited 2018-01-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Chain L
333–360（28 aa）
|
Not recorded | NA SODIUM ION × 2 DKQ 4-chloranylbenzenecarboximidamide × 1 DMS DIMETHYL SULFOXIDE × 3 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；20 mM NaH2PO4, pH 7.5
350 mM NaCl
2mM benzamidine
at a concentration of 10 mg/mL thrombin
|
Resolution 1.27 Å R-free 0.151 |
| 6GBW Thrombin in complex with MI2100 ((S)-N-(2-(aminomethyl)-5-chlorobenzyl)-1-((benzylsulfonyl)-L-arginyl)pyrrolidine-2-carboxamide) Deposited 2018-04-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 DMS DIMETHYL SULFOXIDE × 2 EU5 (2~{S})-~{N}-[[2-(aminomethyl)-5-chloranyl-phenyl]methyl]-1-[(2~{S})-5-carbamimidamido-2-[(phenylmethyl)sulfonylamino]pentanoyl]pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20 mM sodium dihydrogen phosphate ph 7.5
350 mM NaCl
27% PEG 8000
|
Resolution 1.45 Å R-free 0.165 |
| 6GN7 X-ray structure of the complex between human alpha thrombin and NU172, a duplex/quadruplex 26-mer DNA aptamer, in the presence of sodium ions. Deposited 2018-05-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
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 × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Tacsimate 50 % v/v, pH 7.0
|
Resolution 2.80 Å R-free 0.203 |
| 6GWE Crystal structure of Thrombin bound to P2 macrocycle Deposited 2018-06-23 | Different construct Different mutation/modification 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
364–622（259 aa）
Chain B
328–363（36 aa）
|
Not recorded | ODB (10S,14S,17R)-14-(3-carbamimidamidopropyl)-3-[[2-(hydroxymethyl)phenyl]methyl]-5,12,15-tris(oxidanylidene)-19-thia-3,6,13,16-tetrazatricyclo[19.4.0.0^{6,10}]pentacosa-1(21),22,24-triene-17-carboxamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；25% ethylene glycol
100 mM MES pH 6.2
15% w/v PEG 3350
|
Resolution 2.30 Å R-free 0.244 |
| 6GWE Crystal structure of Thrombin bound to P2 macrocycle Deposited 2018-06-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | ODB (10S,14S,17R)-14-(3-carbamimidamidopropyl)-3-[[2-(hydroxymethyl)phenyl]methyl]-5,12,15-tris(oxidanylidene)-19-thia-3,6,13,16-tetrazatricyclo[19.4.0.0^{6,10}]pentacosa-1(21),22,24-triene-17-carboxamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；25% ethylene glycol
100 mM MES pH 6.2
15% w/v PEG 3350
|
Resolution 2.30 Å R-free 0.244 |
| 6HSX Thrombin in Complex with a D-Phe-Pro-diaminopyridine derivative Deposited 2018-10-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 2 GOL GLYCEROL × 2 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 1 GOZ (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[[2,6-bis(azanyl)pyridin-4-yl]methyl]pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20 mM Sodium dihydrogen phosphate pH 7.5, 350 mM NaCl, 27% PEG 8000
|
Resolution 1.56 Å R-free 0.183 |
| 6I51 Thrombin in complex with fragment J02 Deposited 2018-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 DMS DIMETHYL SULFOXIDE × 2 PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 F05 1H-isoindol-3-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；20 mM NaH2PO4, pH 7.5
350 mM NaCl
2 mM benzamidine
at a conc. of 10 mg/ml thrombin
|
Resolution 1.40 Å R-free 0.169 |
| 6P9U Crystal structure of human thrombin mutant W215A Deposited 2019-06-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
333–363（31 aa）
Chain B
364–622（259 aa）
|
Mutation：W215A | ZN ZINC ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；10 mM ZnSO4, 100 mM MES and 25% PEG 550 MME
|
Resolution 3.30 Å R-free 0.308 |
| 6P9U Crystal structure of human thrombin mutant W215A Deposited 2019-06-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain C
333–363（31 aa）
Chain D
364–622（259 aa）
|
Mutation：W215A | ZN ZINC ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；10 mM ZnSO4, 100 mM MES and 25% PEG 550 MME
|
Resolution 3.30 Å R-free 0.308 |
| 6P9U Crystal structure of human thrombin mutant W215A Deposited 2019-06-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain E
333–363（31 aa）
Chain F
364–622（259 aa）
|
Mutation：W215A | ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；10 mM ZnSO4, 100 mM MES and 25% PEG 550 MME
|
Resolution 3.30 Å R-free 0.308 |
| 6P9U Crystal structure of human thrombin mutant W215A Deposited 2019-06-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain G
333–363（31 aa）
Chain H
364–622（259 aa）
|
Mutation：W215A | ZN ZINC ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；10 mM ZnSO4, 100 mM MES and 25% PEG 550 MME
|
Resolution 3.30 Å R-free 0.308 |
| 6PX5 CRYSTAL STRUCTURE OF HUMAN MEIZOTHROMBIN DESF1 MUTANT S195A bound with PPACK Deposited 2019-07-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
364–622（259 aa）
Chain X
212–363（152 aa）
|
Mutation：S195A | ZN ZINC ION × 2 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, HANGING DROP；pH 6.5；293 K；10 mM zinc sulfate, 100 mM MES, pH 6.5, 25% PEG 550 MME
|
Resolution 2.40 Å R-free 0.282 |
| 6PXJ Crystal structure of human thrombin mutant I16T Deposited 2019-07-26 | Different construct Different mutation/modification 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
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；200 mM Mg formate, 20% PEG 3350
|
Resolution 1.70 Å R-free 0.203 |
| 6PXJ Crystal structure of human thrombin mutant I16T Deposited 2019-07-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；200 mM Mg formate, 20% PEG 3350
|
Resolution 1.70 Å R-free 0.203 |
| 6PXQ Crystal structure of human thrombin mutant D194A Deposited 2019-07-26 | Different construct Different mutation/modification 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
331–363（33 aa）
Chain B
364–622（259 aa）
|
Mutation：D194A | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；200 mM di-Na phosphate and 20% PEG 3350
|
Resolution 2.80 Å R-free 0.292 |
| 6ROT Thrombin in complex with MI2105 Deposited 2019-05-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | KDQ (2~{S})-~{N}-[[5-chloranyl-2-(hydroxymethyl)phenyl]methyl]-1-[2-[(phenylmethyl)sulfonylamino]ethanoyl]pyrrolidine-2-carboxamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 1 DMS DIMETHYL SULFOXIDE × 3 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20mM sodium dihydrogen phosphate ph 7.5
350mM NaCl
27% PEG 8000
|
Resolution 1.34 Å R-free 0.157 |
| 6T3M Thrombin in Complex with a D-Phe-Pro-p-phenol derivative Deposited 2019-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MD8 (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(4-hydroxyphenyl)methyl]pyrrolidine-2-carboxamide × 2 PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20 mM NaH2PO4 (pH 7.5), 350 mM NaCl, 27% (w/v) PEG 8000
|
Resolution 1.38 Å R-free 0.158 |
| 6T3Q Thrombin in Complex with a D-Phe-Pro-2-aminopyridine derivative Deposited 2019-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 NA SODIUM ION × 2 M6Q (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(2-azanylpyridin-4-yl)methyl]pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20 mM NaH2PO4 (pH 7.5), 350 mM NaCl, 27% (w/v) PEG8000
|
Resolution 1.33 Å R-free 0.146 |
| 6T4A Thrombin in Complex with a D-Phe-Pro-p-aminopyridine derivative Deposited 2019-10-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 J5K (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(6-azanylpyridin-3-yl)methyl]pyrrolidine-2-carboxamide × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20 mM NaH2PO4 (pH 7.5), 350 mM NaCl, 27% (w/v) PEG8000
|
Resolution 1.31 Å R-free 0.148 |
| 6T52 Thrombin in Complex with a D-Phe-Pro-imidazole derivative Deposited 2019-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 DMS DIMETHYL SULFOXIDE × 1 MJH (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[2-(1~{H}-imidazol-4-yl)ethyl]pyrrolidine-2-carboxamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20 mM NaH2PO4, 350 mM NaCl, 27% (w/v) PEG8000
|
Resolution 1.45 Å R-free 0.161 |
| 6T53 Thrombin in Complex with a D-Phe-Pro-p-benzylamine derivative Deposited 2019-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 DMS DIMETHYL SULFOXIDE × 2 K73 (2~{S})-~{N}-[[4-(aminomethyl)phenyl]methyl]-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]pyrrolidine-2-carboxamide × 1 GOL GLYCEROL × 6 PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20 mM NaH2PO4, 350 mM NaCl, 27% (w/v) PEG8000
|
Resolution 1.35 Å R-free 0.151 |
| 6T54 Thrombin in Complex with a D-Phe-Pro-2-bromothiophene Derivative Deposited 2019-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 DMS DIMETHYL SULFOXIDE × 2 GOL GLYCEROL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MJK (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-bromanylthiophen-2-yl)methyl]pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20 mM NaH2PO4, 350 mM NaCl, 27% (w/v) PEG8000
|
Resolution 1.57 Å R-free 0.170 |
| 6T55 Thrombin in Complex with Methylbenzylamine Deposited 2019-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 02N 1-(4-methylphenyl)methanamine × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20 mM NaH2PO4, 350 mM NaCl, 27% (w/v) PEG8000
|
Resolution 1.39 Å R-free 0.172 |
| 6T56 Thrombin in Complex with Benzylamine Deposited 2019-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 ABN BENZYLAMINE × 2 GOL GLYCEROL × 1 PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20 mM NaH2PO4, 350 mM NaCl, 27% (w/v) PEG8000
|
Resolution 1.31 Å R-free 0.163 |
| 6T57 Thrombin in Complex with a D-Phe-Pro-N-amidinopiperidine Derivative Deposited 2019-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 1 PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 J3I (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(1-carbamimidoylpiperidin-4-yl)methyl]pyrrolidine-2-carboxamide × 1 TFA trifluoroacetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20 mM NaH2PO4, 350 mM NaCl, 27% (w/v) PEG8000
|
Resolution 1.57 Å R-free 0.213 |
| 6T7H Crystal structure of Thrombin in complex with macrocycle N14-PR4-A Deposited 2019-10-22 | Different construct Different mutation/modification 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
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 2 MRQ (14S,17R)-14-(3-carbamimidamidopropyl)-3-(furan-2-ylmethyl)-5,12,15-tris(oxidanylidene)-19-thia-3,6,13,16-tetrazatricyclo[19.4.0.0^{6,10}]pentacosa-1(25),7,9,21,23-pentaene-17-carboxamide × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；18 % w/v PEG 4000
0.1 M Tris pH 9.0
0.3 M Sodium acetate trihydrate
20 % v/v Ethylene glycol
|
Resolution 2.32 Å R-free 0.239 |
| 6T7H Crystal structure of Thrombin in complex with macrocycle N14-PR4-A Deposited 2019-10-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 1 MRQ (14S,17R)-14-(3-carbamimidamidopropyl)-3-(furan-2-ylmethyl)-5,12,15-tris(oxidanylidene)-19-thia-3,6,13,16-tetrazatricyclo[19.4.0.0^{6,10}]pentacosa-1(25),7,9,21,23-pentaene-17-carboxamide × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；18 % w/v PEG 4000
0.1 M Tris pH 9.0
0.3 M Sodium acetate trihydrate
20 % v/v Ethylene glycol
|
Resolution 2.32 Å R-free 0.239 |
| 6T89 Thrombin in complex with (S)-N-(tert-butyl)-4-(3-(3-carbamimidoylphenyl)-2-((2',4'-dimethoxy-[1,1'-biphenyl])-3-sulfonamido)propanoyl)piperazine-1-carboxamide (MI-498) Deposited 2019-10-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | MUQ 4-[(2~{S})-3-(3-carbamimidoylphenyl)-2-[[3-(4-methoxy-2-oxidanyl-phenyl)phenyl]sulfonylamino]propanoyl]-~{N}-methyl-piperazine-1-carboxamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20 mM sodium dihydrogen phosphate ph 7.5
350 mM NaCl
27 % PEG 8000
|
Resolution 2.00 Å R-free 0.215 |
| 6T8A Thrombin in complex with diphenyl ((4-carbamimidoylphenyl)((S)-1-((R)-3-cyclohexyl 2-((phenylmethyl)sulfonamido)propanoyl)pyrrolidine-2-carboxamido)methyl)phosphonate (MI-492) Deposited 2019-10-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | MUZ [(~{R})-(4-carbamimidoylphenyl)-[[(2~{S})-1-[(2~{R})-3-cyclohexyl-2-[(phenylmethyl)sulfonylamino]propanoyl]pyrrolidin-2-yl]carbonylamino]methyl]-phenoxy-phosphinous acid × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20 mM sodium dihydrogen phosphate ph 7.5
350 mM NaCl
27 % PEG 8000
|
Resolution 1.62 Å R-free 0.185 |
| 6TDT Thrombin in Complex with a D-DiPhe-Pro-p-pyridine derivative Deposited 2019-11-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 DMS DIMETHYL SULFOXIDE × 1 LXW (2~{S})-1-[(2~{R})-2-azanyl-3,3-diphenyl-propanoyl]-~{N}-(pyridin-4-ylmethyl)pyrrolidine-2-carboxamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20 mM Sodium dihydrogen phosphate, 350 mM NaCl, 27% (w/v) PEG 8000
|
Resolution 1.53 Å R-free 0.177 |
| 6TKG Tsetse thrombin inhibitor in complex with human alpha-thrombin - orthorhombic form at 12keV Deposited 2019-11-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES pH 7.5, 0.2 M ammonium acetate, 25 % (w/v) PEG 3350
|
Resolution 1.35 Å R-free 0.195 |
| 6TKH Tsetse thrombin inhibitor in complex with human alpha-thrombin - orthorhombic form at 7keV Deposited 2019-11-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | GOL GLYCEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES pH 7.5, 0.2 M ammonium acetate, 25 % (w/v) PEG 3350
|
Resolution 1.90 Å R-free 0.200 |
| 6TKI Tsetse thrombin inhibitor in complex with human alpha-thrombin - tetragonal form at 12.7keV Deposited 2019-11-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 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, SITTING DROP；293 K；0.05 M sodium cacodylate pH 6.5, 0.01 M magnesium sulfate, 2 M ammonium sulfate
|
Resolution 1.80 Å R-free 0.214 |
| 6TKJ Tsetse thrombin inhibitor in complex with human alpha-thrombin - tetragonal form at 7keV Deposited 2019-11-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M sodium cacodylate pH 6.5, 0.01 M magnesium sulfate, 2 M ammonium sulfate
|
Resolution 2.81 Å R-free 0.244 |
| 6TKL Non-cleavable tsetse thrombin inhibitor in complex with human alpha-thrombin Deposited 2019-11-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES pH 7.5, 0.2 M ammonium acetate, 28 % (w/v) PEG 3350
|
Resolution 1.30 Å R-free 0.176 |
| 6V5T Crystal structure of human prethrombin-2 with tryptophans replaced by 5-F-tryptophan Deposited 2019-12-04 | 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 E
333–622（290 aa）
Fragment：Light and heavy chain, residues 333-622
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M Hepes pH 7.5,
25% PEG 8000
|
Resolution 2.10 Å R-free 0.230 |
| 6V64 Crystal structure of human thrombin bound to ppack with tryptophans replaced by 5-F-tryptophan Deposited 2019-12-04 | Different construct Different mutation/modification 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
334–363（30 aa）
Fragment：residues 334-363
Chain B
364–622（259 aa）
Fragment：residues 364-622
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | NA SODIUM ION × 2 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2 M Na/K tartrate pH 7.5
14% PEG 3350
|
Resolution 2.29 Å R-free 0.277 |
| 6Y02 Thrombin in complex with 13k Deposited 2020-02-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 DMS DIMETHYL SULFOXIDE × 2 GOL GLYCEROL × 2 O5Z (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-bromanylfuran-2-yl)methyl]pyrrolidine-2-carboxamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20mM sodium dihydrogen phosphate ph 7.5
350mM NaCl
27% PEG 8000
|
Resolution 1.48 Å R-free 0.164 |
| 6Y9H Thrombin in complex with D-Phe-Pro-m-Trifluoromethylbenzylamide derivative (phe2) Deposited 2020-03-09 | 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 H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 DMS DIMETHYL SULFOXIDE × 1 PO4 PHOSPHATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；20mM sodium dihydrogen phosphate ph 7.5
350mM NaCl
27% PEG 8000
|
Resolution 1.48 Å R-free 0.170 |
| 6YB6 Thrombin in complex with D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative (13c) Deposited 2020-03-16 | 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 H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 DMS DIMETHYL SULFOXIDE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20mM sodium dihydrogen phosphate ph 7.5
350mM NaCl
27% PEG 8000
|
Resolution 1.33 Å R-free 0.153 |
| 6YHG Thrombin in complex with D-Phe-Pro-m-methoxybenzylamide derivative (16a) Deposited 2020-03-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1 DPN D-PHENYLALANINE × 1 PRO PROLINE × 1 SZ4 1-(3-methoxyphenyl)methanamine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20mM sodium dihydrogen phosphate ph 7.5
350mM NaCl
27% PEG 8000
|
Resolution 1.33 Å R-free 0.145 |
| 6YHJ Thrombin in complex with D-Phe-Pro-2-chlorothiophen derivative (16e) Deposited 2020-03-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 OQZ (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-chloranylthiophen-2-yl)methyl]pyrrolidine-2-carboxamide × 2 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20mM sodium dihydrogen phosphate ph 7.5
350mM NaCl
27% PEG 8000
|
Resolution 1.44 Å R-free 0.154 |
| 6YMP Thrombin in complex with 3-((5-(tert-butyl)isoxazol-3-yl)methyl)oxetan-3-amine (j54) Deposited 2020-04-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 DMS DIMETHYL SULFOXIDE × 2 D6Y 3-[(5-tert-butyl-1,2-oxazol-3-yl)methyl]oxetan-3-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20mM sodium dihydrogen phosphate ph 7.5
350mM NaCl
27% PEG 8000
|
Resolution 1.42 Å R-free 0.154 |
| 6YN3 Thrombin in complex with 4-hydroxybenzamide (j89) Deposited 2020-04-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 DMS DIMETHYL SULFOXIDE × 2 HBD 4-HYDROXYBENZAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20mM sodium dihydrogen phosphate pH 7.5
350mM NaCl
27% PEG 8000
|
Resolution 1.49 Å R-free 0.167 |
| 6YQV Thrombin in complex with 5-chlorothiophene-2-sulfonamide (j94) Deposited 2020-04-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 DMS DIMETHYL SULFOXIDE × 3 PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 8K2 5-chloranylthiophene-2-sulfonamide × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20mM sodium dihydrogen phosphate pH 7.5
350mM NaCl
27% PEG 8000
|
Resolution 1.45 Å R-free 0.163 |
| 6YSJ Thrombin in complex with 2-amino-1-(4-bromophenyl)ethan-1-one (j10) Deposited 2020-04-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 DMS DIMETHYL SULFOXIDE × 2 47A 2-amino-1-(4-bromophenyl)ethanone × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20mM sodium dihydrogen phosphate pH 7.5
350mM NaCl
27% PEG 8000
|
Resolution 1.45 Å R-free 0.168 |
| 6YSX Thrombin in complex with 4-amino-N-(5-methylisoxazol-3-yl)benzenesulfonamide (j80) Deposited 2020-04-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 DMS DIMETHYL SULFOXIDE × 2 PO4 PHOSPHATE ION × 1 08D Sulfamethoxazole × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20mM sodium dihydrogen phosphate pH 7.5
350mM NaCl
27% PEG 8000
|
Resolution 1.48 Å R-free 0.162 |
| 6Z48 Crystal structure of Thrombin in complex with macrocycle X1vE Deposited 2020-05-23 | Different construct Different mutation/modification 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
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 1 X1V 5-chloranyl-N-[[(4S,15R)-2,5,13,16-tetrakis(oxidanylidene)-15-propan-2-yl-9,10-dithia-3,6,14,17-tetrazabicyclo[17.3.1]tricosa-1(22),19(23),20-trien-4-yl]methyl]thiophene-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；100 mM MOPS/sodium HEPES pH 7.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD
|
Resolution 2.27 Å R-free 0.242 |
| 6Z48 Crystal structure of Thrombin in complex with macrocycle X1vE Deposited 2020-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | NA SODIUM ION × 1 X1V 5-chloranyl-N-[[(4S,15R)-2,5,13,16-tetrakis(oxidanylidene)-15-propan-2-yl-9,10-dithia-3,6,14,17-tetrazabicyclo[17.3.1]tricosa-1(22),19(23),20-trien-4-yl]methyl]thiophene-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；100 mM MOPS/sodium HEPES pH 7.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD
|
Resolution 2.27 Å R-free 0.242 |
| 6Z48 Crystal structure of Thrombin in complex with macrocycle X1vE Deposited 2020-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
328–363（36 aa）
Chain D
364–622（259 aa）
|
Not recorded | NA SODIUM ION × 1 X1V 5-chloranyl-N-[[(4S,15R)-2,5,13,16-tetrakis(oxidanylidene)-15-propan-2-yl-9,10-dithia-3,6,14,17-tetrazabicyclo[17.3.1]tricosa-1(22),19(23),20-trien-4-yl]methyl]thiophene-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；100 mM MOPS/sodium HEPES pH 7.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD
|
Resolution 2.27 Å R-free 0.242 |
| 6Z48 Crystal structure of Thrombin in complex with macrocycle X1vE Deposited 2020-05-23 | 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 E
328–363（36 aa）
Chain F
364–622（259 aa）
|
Not recorded | NA SODIUM ION × 1 X1V 5-chloranyl-N-[[(4S,15R)-2,5,13,16-tetrakis(oxidanylidene)-15-propan-2-yl-9,10-dithia-3,6,14,17-tetrazabicyclo[17.3.1]tricosa-1(22),19(23),20-trien-4-yl]methyl]thiophene-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；100 mM MOPS/sodium HEPES pH 7.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD
|
Resolution 2.27 Å R-free 0.242 |
| 6Z8V X-ray structure of the complex between human alpha thrombin and a thrombin binding aptamer variant (TBA-3L), which contains 1-beta-D-lactopyranosyl residue in the side chain of Thy3 at N3. Deposited 2020-06-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
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 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；200 mM KCl, 35% v/v pentaerythritol propoxylate, 50 mM HEPES, pH 7.5
|
Resolution 1.58 Å R-free 0.206 |
| 6Z8W X-ray structure of the complex between human alpha thrombin and a thrombin binding aptamer variant (TBA-3G), which contains 1-beta-D-glucopyranosyl residue in the side chain of Thy3 at N3. Deposited 2020-06-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
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 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；200 mM KCl, 35% v/v pentaerythritol propoxylate, 50 mM HEPES, pH 7.5
|
Resolution 1.73 Å R-free 0.207 |
| 6Z8X X-ray structure of the complex between human alpha thrombin and a thrombin binding aptamer variant (TBA-3Leu), which contains leucyl amide in the side chain of Thy3 at N3. Deposited 2020-06-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
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 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；18% v/v 2-propanol, 18% w/v PEG 4000, 100 mM tri-sodium citrate, pH 5.6
|
Resolution 2.53 Å R-free 0.291 |
| 6ZGO Thrombin in complex with D-Phe-Pro-2-chlorofuran derivative (13l) Deposited 2020-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 DMS DIMETHYL SULFOXIDE × 3 QKE (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-chloranylfuran-2-yl)methyl]pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20mM sodium dihydrogen phosphate ph 7.5
350mM NaCl
27% PEG 8000
|
Resolution 1.79 Å R-free 0.225 |
| 6ZUG Crystal Structure of Thrombin in complex with compound10 Deposited 2020-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–621（258 aa）
Chain L
333–361（29 aa）
|
Not recorded | QPW 2-[(3-chlorophenyl)methylamino]-7-methoxy-~{N}-[[(3~{S})-oxolan-3-yl]methyl]-~{N}-propyl-1,3-benzoxazole-5-carboxamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；283 K；0.02 M phosphate buffer pH 7.5,
27% PEG 8000, 100 mM NaCl
|
Resolution 1.80 Å R-free 0.212 |
| 6ZUH Crystal Structure of Thrombin in complex with compound17 Deposited 2020-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | N6H [2-[(3-chlorophenyl)methylamino]-7-methoxy-1,3-benzoxazol-5-yl]-(2,2-dimethylmorpholin-4-yl)methanone × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；283 K；0.02 M phosphate buffer pH 7.5,
27% PEG 8000, 100 mM NaCl
|
Resolution 1.70 Å R-free 0.218 |
| 6ZUN Crystal Structure of Thrombin in complex with compound20a Deposited 2020-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | QQ5 [2-[(3-chlorophenyl)methylamino]-7-methoxy-1,3-benzoxazol-5-yl]-[(3~{R},4~{R})-3-methyl-4-oxidanyl-piperidin-1-yl]methanone × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；283 K；0.02 M phosphate buffer pH 7.5,
27% PEG 8000, 100 mM NaCl
|
Resolution 1.79 Å R-free 0.262 |
| 6ZUU Crystal structure of Thrombin in complex with compound30 Deposited 2020-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | QQN [2-[(3-chlorophenyl)methylamino]-4-methoxy-1,3-benzoxazol-6-yl]-[(3~{R},4~{R})-3-methyl-4-oxidanyl-piperidin-1-yl]methanone × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；283 K；0.02 M phosphate buffer pH 7.5,
27% PEG 8000, 100 mM NaCl
|
Resolution 1.94 Å R-free 0.212 |
| 6ZUW Crystal Structure of Thrombin in complex with compound40 Deposited 2020-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | QQK [2-[[(1~{R})-1-(3-chlorophenyl)ethyl]amino]-7-methoxy-1,3-benzoxazol-5-yl]-[(2~{S},5~{R})-5-ethyl-2-(2-hydroxyethyl)-2-methyl-morpholin-4-yl]methanone × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；283 K；0.02 M phosphate buffer pH 7.5,
27% PEG 8000, 100 mM NaCl
|
Resolution 2.00 Å R-free 0.213 |
| 6ZUX Crystal Structure of Thrombin in complex with compound42a Deposited 2020-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | QQE [2-[[(1~{R})-1-(3-chlorophenyl)ethyl]amino]-7-methoxy-1,3-benzoxazol-5-yl]-[(2~{S},5~{S})-5-(2-hydroxyethyl)-2-methyl-morpholin-4-yl]methanone × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；283 K；0.02 M phosphate buffer pH 7.5,
27% PEG 8000, 100 mM NaCl
|
Resolution 1.94 Å R-free 0.206 |
| 6ZV7 Crystal Structure of Thrombin in complex with compound42b Deposited 2020-07-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 QQW [2-[[(1~{R})-1-(3-chlorophenyl)ethyl]amino]-7-methoxy-1,3-benzoxazol-5-yl]-[(2~{R},5~{R})-5-(2-hydroxyethyl)-2-methyl-morpholin-4-yl]methanone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；283 K；0.02 M phosphate buffer pH 7.5,
27% PEG 8000, 100 mM NaCl
|
Resolution 1.94 Å R-free 0.190 |
| 6ZV8 Crystal Structure of Thrombin in complex with compound51 Deposited 2020-07-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：THE MAJORITY OF THE SEQUENCE
Chain L
328–363（36 aa）
Fragment：POTENIALLY THE FIRST EXON
|
Not recorded | QQT [2-[[(1~{S})-1-(3-chlorophenyl)-2-fluoranyl-ethyl]amino]-7-methoxy-1,3-benzoxazol-5-yl]-[(2~{S},5~{S})-5-(2-hydroxyethyl)-2-methyl-morpholin-4-yl]methanone × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；283 K；0.02 M phosphate buffer pH 7.5,
27% PEG 8000, 100 mM NaCl
|
Resolution 1.70 Å R-free 0.247 |
| 7AC9 Thrombin in complex with D-arginine (j77) Deposited 2020-09-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 DMS DIMETHYL SULFOXIDE × 2 PO4 PHOSPHATE ION × 1 DAR D-ARGININE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20mM sodium dihydrogen phosphate pH 7.5
350mM NaCl
27% PEG 8000
|
Resolution 1.39 Å R-free 0.163 |
| 7KME CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN INHIBITED WITH SEL2711. Deposited 1999-02-26 | 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 H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.3；pH 7.30
|
Resolution 2.10 Å |
| 7MJ5 complex of human thrombin with XC-43 Deposited 2021-04-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 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；298 K；0.2 M magnesium acetate, 9 % PEG 8000
|
Resolution 2.15 Å R-free 0.193 |
| 7MJ5 complex of human thrombin with XC-43 Deposited 2021-04-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
328–363（36 aa）
Chain C
364–622（259 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；298 K；0.2 M magnesium acetate, 9 % PEG 8000
|
Resolution 2.15 Å R-free 0.193 |
| 7MJ5 complex of human thrombin with XC-43 Deposited 2021-04-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
328–363（36 aa）
Chain E
364–622（259 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；298 K；0.2 M magnesium acetate, 9 % PEG 8000
|
Resolution 2.15 Å R-free 0.193 |
| 7MJ5 complex of human thrombin with XC-43 Deposited 2021-04-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
328–363（36 aa）
Chain G
364–622（259 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；298 K；0.2 M magnesium acetate, 9 % PEG 8000
|
Resolution 2.15 Å R-free 0.193 |
| 7MJ5 complex of human thrombin with XC-43 Deposited 2021-04-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
328–363（36 aa）
Chain J
364–622（259 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；298 K；0.2 M magnesium acetate, 9 % PEG 8000
|
Resolution 2.15 Å R-free 0.193 |
| 7MJ5 complex of human thrombin with XC-43 Deposited 2021-04-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain K
328–363（36 aa）
Chain M
364–622（259 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；298 K；0.2 M magnesium acetate, 9 % PEG 8000
|
Resolution 2.15 Å R-free 0.193 |
| 7NTU X-ray structure of the complex between human alpha thrombin and two duplex/quadruplex aptamers: NU172 and HD22_27mer Deposited 2021-03-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
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 × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；26% w/v PEG 3350, 0.2 M ammonium acetate and 0.1 M Bis-Tris pH 6.5
|
Resolution 3.10 Å R-free 0.257 |
| 7NTU X-ray structure of the complex between human alpha thrombin and two duplex/quadruplex aptamers: NU172 and HD22_27mer Deposited 2021-03-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain C
328–363（36 aa）
Chain D
364–622（259 aa）
|
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 × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；26% w/v PEG 3350, 0.2 M ammonium acetate and 0.1 M Bis-Tris pH 6.5
|
Resolution 3.10 Å R-free 0.257 |
| 7PHX Tsetse thrombin inhibitor in complex with human alpha-thrombin - acid-stable sulfotyrosine analogue Deposited 2021-08-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 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, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 0.2 M ammonium acetate,
25% (w/v) PEG 3350
|
Resolution 1.80 Å R-free 0.221 |
| 7SR9 Human alpha-thrombin with 180- and 220- loops replaced with homologous loops from protein C Deposited 2021-11-08 | Different construct Different mutation/modification 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
329–363（35 aa）
Fragment：UNP residues 328-363
Chain B
364–619（256 aa）
Fragment：UNP residues 364-622
|
Mutation：Y184A I, K 184B L, K186D, P186 deleted, D186A deleted, E186B deleted, G188Q, D 221A G, R221L, D222L, G223H, K224N | SO4 SULFATE ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris, pH 8.5, 0.2 M lithium sulfate, 30% PEG4000
|
Resolution 2.10 Å R-free 0.227 |
| 7TPP Cryo-em structure of human prothrombin:prothrombinase at 4.1 Angstrom resolution Deposited 2022-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
44–622（579 aa）
Fragment：UNP residues 44-622
|
Mutation：S525A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；20mM Hepes, 150mM NaCl, 5mM CaCl2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 7ZKL X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (TBA-NNp/DDp) - Crystal form alpha Deposited 2022-04-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
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 LMR (2S)-2-hydroxybutanedioic acid × 1 JL0 3-[13-methyl-5,7,12,14-tetrakis(oxidanylidene)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1(15),2,4(16),8,10-pentaen-6-yl]propyl 3-[5,7,12,14-tetrakis(oxidanylidene)-13-(3-oxidanylpropyl)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1,3,8(16),9,11(15)-pentaen-6-yl]propyl hydrogen phosphate × 1 JKR 3-[5-[3-bis(oxidanyl)phosphanyloxypropoxy]naphthalen-1-yl]oxypropyl 3-(5-oxidanylnaphthalen-1-yl)oxypropyl hydrogen phosphate × 1 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Tacsimate 46% v/v, pH 7.0
|
Resolution 3.18 Å R-free 0.231 |
| 7ZKM X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (TBA-NNp/DDp) - Crystal form beta Deposited 2022-04-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
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 JL0 3-[13-methyl-5,7,12,14-tetrakis(oxidanylidene)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1(15),2,4(16),8,10-pentaen-6-yl]propyl 3-[5,7,12,14-tetrakis(oxidanylidene)-13-(3-oxidanylpropyl)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1,3,8(16),9,11(15)-pentaen-6-yl]propyl hydrogen phosphate × 2 JKR 3-[5-[3-bis(oxidanyl)phosphanyloxypropoxy]naphthalen-1-yl]oxypropyl 3-(5-oxidanylnaphthalen-1-yl)oxypropyl hydrogen phosphate × 2 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG 4000 20% w/v, 2-propanol 20% v/v, trisodium citrate 0.1 M, pH 5.6
|
Resolution 2.00 Å R-free 0.252 |
| 7ZKN X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (TBA-NNp/DDp) - Crystal form gamma Deposited 2022-04-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 JL0 3-[13-methyl-5,7,12,14-tetrakis(oxidanylidene)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1(15),2,4(16),8,10-pentaen-6-yl]propyl 3-[5,7,12,14-tetrakis(oxidanylidene)-13-(3-oxidanylpropyl)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1,3,8(16),9,11(15)-pentaen-6-yl]propyl hydrogen phosphate × 2 JKR 3-[5-[3-bis(oxidanyl)phosphanyloxypropoxy]naphthalen-1-yl]oxypropyl 3-(5-oxidanylnaphthalen-1-yl)oxypropyl hydrogen phosphate × 2 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 3350 25% w/v, ammonium acetate 0.2 M, Bis-Tris 0.1 M, pH 6.5
|
Resolution 3.03 Å R-free 0.243 |
| 7ZKN X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (TBA-NNp/DDp) - Crystal form gamma Deposited 2022-04-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain C
328–363（36 aa）
Chain D
364–622（259 aa）
|
Not recorded | 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 JL0 3-[13-methyl-5,7,12,14-tetrakis(oxidanylidene)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1(15),2,4(16),8,10-pentaen-6-yl]propyl 3-[5,7,12,14-tetrakis(oxidanylidene)-13-(3-oxidanylpropyl)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1,3,8(16),9,11(15)-pentaen-6-yl]propyl hydrogen phosphate × 2 JKR 3-[5-[3-bis(oxidanyl)phosphanyloxypropoxy]naphthalen-1-yl]oxypropyl 3-(5-oxidanylnaphthalen-1-yl)oxypropyl hydrogen phosphate × 2 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 3350 25% w/v, ammonium acetate 0.2 M, Bis-Tris 0.1 M, pH 6.5
|
Resolution 3.03 Å R-free 0.243 |
| 7ZKO X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (TBA-NNp/DDp) - Crystal form delta Deposited 2022-04-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
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 JL0 3-[13-methyl-5,7,12,14-tetrakis(oxidanylidene)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1(15),2,4(16),8,10-pentaen-6-yl]propyl 3-[5,7,12,14-tetrakis(oxidanylidene)-13-(3-oxidanylpropyl)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1,3,8(16),9,11(15)-pentaen-6-yl]propyl hydrogen phosphate × 1 JKR 3-[5-[3-bis(oxidanyl)phosphanyloxypropoxy]naphthalen-1-yl]oxypropyl 3-(5-oxidanylnaphthalen-1-yl)oxypropyl hydrogen phosphate × 1 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 3350 30% w/v, 0.2 M sodium malonate, pH 7.0
|
Resolution 2.50 Å R-free 0.295 |
| 8ASE Crystal structure of Thrombin in complex with macrocycle T3 Deposited 2022-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain H
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NWR (8~{S},14~{S},18~{E})-8-[(4-chlorophenyl)methyl]-3,21-dithia-7,10,16-triazatricyclo[21.2.2.1^{10,14}]octacosa-1(26),18,23(27),24-tetraene-6,9,15-trione × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100 mM Bis-Tris,
200 mM ammonium sulfate, 25% w/v PEG 3350 pH 5.5
|
Resolution 2.55 Å R-free 0.250 |
| 8ASE Crystal structure of Thrombin in complex with macrocycle T3 Deposited 2022-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | NWR (8~{S},14~{S},18~{E})-8-[(4-chlorophenyl)methyl]-3,21-dithia-7,10,16-triazatricyclo[21.2.2.1^{10,14}]octacosa-1(26),18,23(27),24-tetraene-6,9,15-trione × 1 SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100 mM Bis-Tris,
200 mM ammonium sulfate, 25% w/v PEG 3350 pH 5.5
|
Resolution 2.55 Å R-free 0.250 |
| 8ASF Crystal structure of Thrombin in complex with macrocycle T1 Deposited 2022-08-19 | Different construct Different mutation/modification 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
364–622（259 aa）
Chain L
328–363（36 aa）
|
Not recorded | NWF 5-chloranyl-~{N}-[[(9~{S},15~{R})-8,14,17-tris(oxidanylidene)-3,20-dithia-7,13,16-triazatetracyclo[20.2.2.1^{5,7}.1^{9,13}]octacosa-1(25),22(26),23-trien-15-yl]methyl]thiophene-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；100 mM sodium acetate, 50 mM magnesium chloride hexahydrate, 8% w/v PEG
3350, pH 4.5
|
Resolution 2.58 Å R-free 0.240 |
| 8ASF Crystal structure of Thrombin in complex with macrocycle T1 Deposited 2022-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | NWF 5-chloranyl-~{N}-[[(9~{S},15~{R})-8,14,17-tris(oxidanylidene)-3,20-dithia-7,13,16-triazatetracyclo[20.2.2.1^{5,7}.1^{9,13}]octacosa-1(25),22(26),23-trien-15-yl]methyl]thiophene-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；100 mM sodium acetate, 50 mM magnesium chloride hexahydrate, 8% w/v PEG
3350, pH 4.5
|
Resolution 2.58 Å R-free 0.240 |
| 8BW5 X-ray structure of the complex between human alpha thrombin and the duplex/quadruplex aptamer M08s-1_41mer Deposited 2022-12-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Fragment：THROMBIN HEAVY CHAIN, UNP RESIDUES 364-622
Chain L
328–363（36 aa）
|
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 × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 8000 20% w/v, magnesium acetate 0.2 M, sodium cacodylate 0.1 M, pH 6.5
|
Resolution 2.80 Å R-free 0.252 |
| 8BWW Targeting Toll-like receptor-driven systemic inflammation by engineering an innate structural fold into drugs Deposited 2022-12-07 | 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
605–622（18 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 4.5；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition
1.6 mM sHVF18, 50 % v/v TFE, 10 % v/v D2O, 200 uM DSS, 0.02 % v/v sodium azide, trifluoroethanol/water | trifluoroethanol/water
|
Resolution not provided |
| 8KME CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN INHIBITED WITH SEL2770. Deposited 1999-03-21 | 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 1
328–363（36 aa）
Fragment：LIGHT CHAIN
Chain 2
364–622（259 aa）
Fragment：HEAVY CHAIN
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.3；0.1 M SODIUM PHASPATE BUFFER, PH 7.3
28 % PEG 8000
|
Resolution 2.10 Å |
| 8RTN Human thrombin in complex with a trivalent inhibitor Deposited 2024-01-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
1–622（622 aa）
Chain L
1–622（622 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, SITTING DROP；293 K；0.2 M lithium citrate tribasic tetrahydrate
20% (w/v) PEG 3350
|
Resolution 2.51 Å R-free 0.213 |
| 8TQS Complex of human thrombin (S195A) bound to a bivalent inhibitor comprised of DNA Aptamer HD22 conjugated to Dabigatran with a linker. Deposited 2023-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
320–360（41 aa）
|
Mutation：S195A | MG MAGNESIUM ION × 1 NA SODIUM ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 4CC N-[(2-{[(4-carbamimidoylphenyl)amino]methyl}-1-methyl-1H-benzimidazol-5-yl)carbonyl]-N-pyridin-2-yl-beta-alanine × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.1 M MES monohydrate pH 6, 22% (v/v) polyethylene glycol 400 (Hampton PEGRx1 #08)
|
Resolution 2.21 Å R-free 0.245 |
| 8UF7 Cryo-EM structure of POmAb, a Type-I anti-prothrombin antiphospholipid antibody, bound to kringle-1 of human prothrombin Deposited 2023-10-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
44–622（579 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9C50 Replacement of a single residue changes the primary specificity of thrombin Deposited 2024-06-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–363（36 aa）
Chain B
364–622（259 aa）
|
Not recorded | NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.1 M succinic acid, 15% PEG3350
|
Resolution 2.50 Å R-free 0.245 |
| 9C50 Replacement of a single residue changes the primary specificity of thrombin Deposited 2024-06-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
328–363（36 aa）
Chain D
364–622（259 aa）
|
Not recorded | NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.1 M succinic acid, 15% PEG3350
|
Resolution 2.50 Å R-free 0.245 |
| 9CLN Cryo-EM model derived from localized reconstruction of human adenovirus 5 (Ad5)-hexon-FII complex at 3.9A resolution Deposited 2024-07-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain Z
1–622（622 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CA CALCIUM ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.13 Å |
| 9CLS Cryo-EM model derived from localized reconstruction of human adenovirus 6 (Ad6)-hexon-FII complex Deposited 2024-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain Z
1–622（622 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CA CALCIUM ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 9CMO Cryo-EM model derived from localized reconstruction of Ad657-hexon-FII complex at 4.14A resolution Deposited 2024-07-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain Z
1–622（622 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CA CALCIUM ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.17 Å |
| 9CTH Preliminary map of the Prothrombin-prothrombinase complex on nano discs Deposited 2024-07-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain D
44–622（579 aa）
Fragment：UNP residues 44-622
|
Mutation：S525A | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；20 mM HEPES, 150 mM NaCl, and 5 mM CaCl2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.47 Å |
| 9H5N Crystal structure of Thrombin in complex with a Chlorothiophene-based inhibitor, CP3, discovered by a novel rapid nanoscale library screening. Deposited 2024-10-22 | Different construct Different mutation/modification 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
315–363（49 aa）
Chain B
364–622（259 aa）
|
Not recorded | A1ISR ~{N}-[(3~{S})-4-[3-(2-azanyl-2-oxidanylidene-ethyl)sulfanylpropylamino]-4-oxidanylidene-3-(2-phenylethanoylamino)butyl]-5-chloranyl-thiophene-2-carboxamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Sodium-HEPES, 100 mM MOPS pH 7.5, 100 mM amino acids (20 mM D-L
glutamic acid monohydrate, 20mM D-L alanine, 20 mM glycine, 20mM D-L lysine
monohydrochloride, 20mM D-L serine) 12,5% v/v MPD;
12,5% w/v PEG1000,
12,5% w/v PEG3350
|
Resolution 3.10 Å R-free 0.284 |
| 9H5N Crystal structure of Thrombin in complex with a Chlorothiophene-based inhibitor, CP3, discovered by a novel rapid nanoscale library screening. Deposited 2024-10-22 | Different construct Different mutation/modification 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
315–363（49 aa）
Chain D
364–622（259 aa）
|
Not recorded | A1ISR ~{N}-[(3~{S})-4-[3-(2-azanyl-2-oxidanylidene-ethyl)sulfanylpropylamino]-4-oxidanylidene-3-(2-phenylethanoylamino)butyl]-5-chloranyl-thiophene-2-carboxamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Sodium-HEPES, 100 mM MOPS pH 7.5, 100 mM amino acids (20 mM D-L
glutamic acid monohydrate, 20mM D-L alanine, 20 mM glycine, 20mM D-L lysine
monohydrochloride, 20mM D-L serine) 12,5% v/v MPD;
12,5% w/v PEG1000,
12,5% w/v PEG3350
|
Resolution 3.10 Å R-free 0.284 |
| 9H79 Crystal structure of Thrombin in complex with a Chlorothiophene-based inhibitor, CP2, discovered by a novel rapid nanoscale library screening. Deposited 2024-10-27 | Different construct Different mutation/modification 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
315–363（49 aa）
Chain B
364–622（259 aa）
|
Not recorded | A1ITQ ~{N}-[(3~{S})-4-[3-(2-azanyl-2-oxidanylidene-ethyl)sulfanylpropylamino]-3-[2-(3-chlorophenyl)ethanoylamino]-4-oxidanylidene-butyl]-5-chloranyl-thiophene-2-carboxamide × 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；293 K；100 mM Tris, 200 mM Lithium chloride pH 8.0 and 20 % w/v PEG 6000
|
Resolution 3.00 Å R-free 0.266 |
| 9H79 Crystal structure of Thrombin in complex with a Chlorothiophene-based inhibitor, CP2, discovered by a novel rapid nanoscale library screening. Deposited 2024-10-27 | Different construct Different mutation/modification 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
315–363（49 aa）
Chain D
364–622（259 aa）
|
Not recorded | A1ITQ ~{N}-[(3~{S})-4-[3-(2-azanyl-2-oxidanylidene-ethyl)sulfanylpropylamino]-3-[2-(3-chlorophenyl)ethanoylamino]-4-oxidanylidene-butyl]-5-chloranyl-thiophene-2-carboxamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris, 200 mM Lithium chloride pH 8.0 and 20 % w/v PEG 6000
|
Resolution 3.00 Å R-free 0.266 |
| 9H79 Crystal structure of Thrombin in complex with a Chlorothiophene-based inhibitor, CP2, discovered by a novel rapid nanoscale library screening. Deposited 2024-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain E
315–363（49 aa）
Chain F
364–622（259 aa）
|
Not recorded | A1ITQ ~{N}-[(3~{S})-4-[3-(2-azanyl-2-oxidanylidene-ethyl)sulfanylpropylamino]-3-[2-(3-chlorophenyl)ethanoylamino]-4-oxidanylidene-butyl]-5-chloranyl-thiophene-2-carboxamide × 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；293 K；100 mM Tris, 200 mM Lithium chloride pH 8.0 and 20 % w/v PEG 6000
|
Resolution 3.00 Å R-free 0.266 |
| 9H79 Crystal structure of Thrombin in complex with a Chlorothiophene-based inhibitor, CP2, discovered by a novel rapid nanoscale library screening. Deposited 2024-10-27 | 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 G
315–363（49 aa）
Chain H
364–622（259 aa）
|
Not recorded | A1ITQ ~{N}-[(3~{S})-4-[3-(2-azanyl-2-oxidanylidene-ethyl)sulfanylpropylamino]-3-[2-(3-chlorophenyl)ethanoylamino]-4-oxidanylidene-butyl]-5-chloranyl-thiophene-2-carboxamide × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris, 200 mM Lithium chloride pH 8.0 and 20 % w/v PEG 6000
|
Resolution 3.00 Å R-free 0.266 |
| 9R8Q Structure of thrombin bound to BAY 3389934 Deposited 2025-05-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
364–622（259 aa）
Chain L
333–361（29 aa）
Fragment：RESIDUES 333-361
|
Not recorded | A1JDJ 2-(1-methylimidazol-2-yl)ethyl (2~{S})-3-[(5-chloranylthiophen-2-yl)carbonylamino]-2-[[2-ethyl-3-[(3~{S})-3-oxidanyl-2-oxidanylidene-pyrrolidin-1-yl]phenyl]sulfonylamino]propanoate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 3 DMS DIMETHYL SULFOXIDE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.02M phosphate buffer at pH 7.5, 27% PEG 8000 and 100mM sodium chloride. Thrombin seeds were added to the final drop
|
Resolution 1.80 Å R-free 0.200 |
| 9YQ8 Cryo-EM complex of meizothrombinDESF1, factor Xa, and factor Va Deposited 2025-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain H
364–620（257 aa）
Chain L
214–361（148 aa）
Fragment：kringle 2/A-chain
|
Mutation：S525A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.84 Å |
475 other PDB entries and 564 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | THRB_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–289； UniProt 334–622 |
