HUMAN ALPHA-THROMBIN, LIGHT CHAIN
OrganismNot specified
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count | Chain A； UniProt 328–363 Chain B； UniProt 364–622 | Fragment：THROMBIN LIGHT CHAIN Fragment：THROMBIN HEAVY CHAIN | HUMAN FACTOR V, A2-B DOMAIN LINKER × 1 （P12259） 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 |
| 2 | Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count | Chain C； UniProt 328–363 Chain D； UniProt 364–622 | Fragment：THROMBIN LIGHT CHAIN Fragment：THROMBIN HEAVY CHAIN | HUMAN FACTOR V, A2-B DOMAIN LINKER × 1 （P12259） 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 |
| 3 | Other combination Heteromer Protein × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count | Chain E； UniProt 328–363 Chain F； UniProt 364–622 | Fragment：THROMBIN LIGHT CHAIN Fragment：THROMBIN HEAVY CHAIN | HUMAN FACTOR V, A2-B DOMAIN LINKER × 1 （P12259） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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 |
| 4 | Other combination Heteromer Protein × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count | Chain G； UniProt 328–363 Chain H； UniProt 364–622 | Fragment：THROMBIN LIGHT CHAIN Fragment：THROMBIN HEAVY CHAIN | HUMAN FACTOR V, A2-B DOMAIN LINKER × 1 （P12259） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-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 |
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 3P70 | 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
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 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
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 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 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 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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 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 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 mutation/modification Different oligomeric state 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 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 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 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 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 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 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 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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 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 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 mutation/modification Different oligomeric state 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 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 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 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 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 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 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 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 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 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 mutation/modification Different oligomeric state 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
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 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 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 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 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 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 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 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 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 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 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 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 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 mutation/modification Different oligomeric state 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 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 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 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 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 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 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 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 mutation/modification Different oligomeric state 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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 mutation/modification Different oligomeric state 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 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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 mutation/modification Different oligomeric state 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 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 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 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 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 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 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 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 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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 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 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 |
| 2BDY thrombin in complex with inhibitor Deposited 2005-10-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
334–622（289 aa）
Fragment：Heavy and light chain, residues 334-622
|
Not recorded | 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 |
| 2BVR Human thrombin complexed with fragment-based small molecules occupying the S1 pocket Deposited 2005-07-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 mutation/modification Different oligomeric state 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 |
| 3PMH Mechanism of Sulfotyrosine-Mediated Glycoprotein Ib Interaction with Two Distinct alpha-Thrombin Sites Deposited 2010-11-16 | Different construct 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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）
|
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 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 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 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 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 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 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 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 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 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 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 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 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
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 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）
|
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 mutation/modification 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 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 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 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 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 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 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 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 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 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 561 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | THRB_HUMAN |
| Isoform | — |
| PDB entities | 1, 2 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–36； UniProt 328–363 Author chain C； PDBConstruct 1–36； UniProt 328–363 Author chain E； PDBConstruct 1–36； UniProt 328–363 Author chain G； PDBConstruct 1–36； UniProt 328–363 Author chain B； PDBConstruct 1–259； UniProt 364–622 Author chain D； PDBConstruct 1–259； UniProt 364–622 Author chain F； PDBConstruct 1–259； UniProt 364–622 Author chain H； PDBConstruct 1–259； UniProt 364–622 |
