COAGULATION FACTOR X, HEAVY CHAIN
Homo sapiens
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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 235–468 Chain B； UniProt 128–178 | Fragment：HEAVY CHAIN Fragment：LIGHT CHAIN | CA CALCIUM ION × 2 237 (2R,4R)-N~1~-(4-CHLOROPHENYL)-N~2~-[3-FLUORO-2'-(METHYLSULFONYL)BIPHENYL-4-YL]-4-METHOXYPYRROLIDINE-1,2-DICARBOXAMIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions | Resolution 1.50 Å R-free 0.267 |
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 2PR3 | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1C5M 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 homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain D
235–488（254 aa）
Fragment：HEAVY CHAIN
Chain F
84–179（96 aa）
Fragment：LIGHT CHAIN
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；crystallization conditions : Crystals of truncated human factor Xa were
grown in hanging drops from equal volumes of protein solution
(5.0 mg/ml in 20 mM Hepes, 50 mM ammonimum sulfate, pH 8.0) and well
solution (25 % PEG 5K, 0.10 M Hepes, 0.2 M ammonium sulfate, pH 7.5)., VAPOR DIFFUSION
|
Resolution 1.95 Å R-free 0.307 |
| 1EZQ CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR XA COMPLEXED WITH RPR128515 Deposited 2000-05-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Fragment：ACTIVATED FACTOR XA, HEAVY CHAIN
Chain B
46–179（134 aa）
Fragment：FACTOR X LIGHT CHAIN
|
Not recorded | CA CALCIUM ION × 1 RPR 3-[(3'-AMINOMETHYL-BIPHENYL-4-CARBONYL)-AMINO]-2-(3-CARBAMIMIDOYL-BENZYL)-BUTYRIC ACID METHYL ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；292 K；18-20% PEG 600, 50mM Mes-NaOH, 1mM RPR128515, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 2.20 Å R-free 0.267 |
| 1F0R CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR XA COMPLEXED WITH RPR208815 Deposited 2000-05-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Fragment：ACTIVATED FACTOR XA, HEAVY CHAIN
Chain B
46–179（134 aa）
Fragment：FACTOR X LIGHT CHAIN
|
Not recorded | CA CALCIUM ION × 1 815 THIENO[3,2-B]PYRIDINE-2-SULFONIC ACID [1-(1-AMINO-ISOQUINOLIN-7-YLMETHYL)-2-OXO-PYRROLDIN-3-YL]-AMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；292 K；18-22%PEG 600, 50mM Mes-NaOH, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 2.10 Å R-free 0.263 |
| 1F0S Crystal Structure of Human Coagulation Factor XA Complexed with RPR208707 Deposited 2000-05-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Fragment：ACTIVATED FACTOR XA, HEAVY CHAIN
Chain B
46–179（134 aa）
Fragment：FACTOR X LIGHT CHAIN
|
Not recorded | CA CALCIUM ION × 1 PR2 THIENO[3,2-B]PYRIDINE-2-SULFONIC ACID [2-OXO-1-(1H-PYRROLO[2,3-C]PYRIDIN-2-YLMETHYL)-PYRROLIDIN-3-YL]-AMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；292 K；18-22%PEG 600, 50mM Mes-NaOH, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 2.10 Å R-free 0.263 |
| 1FAX COAGULATION FACTOR XA INHIBITOR COMPLEX Deposited 1996-08-23 | Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–481（247 aa）
Chain L
84–179（96 aa）
|
Mutation：PROTEOLYTIC CLEAVAGE PRODUCT, GLA DOMAIN, RESIDUES 1 - 44 OF THE LIGHT CHAIN, ARE REMOVED Mutation：PROTEOLYTIC CLEAVAGE PRODUCT, GLA DOMAIN, RESIDUES 1 - 44 OF THE LIGHT CHAIN, ARE REMOVED | CA CALCIUM ION × 1 DX9 (2S)-3-(7-carbamimidoylnaphthalen-2-yl)-2-[4-({(3R)-1-[(1Z)-ethanimidoyl]pyrrolidin-3-yl}oxy)phenyl]propanoic acid × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.00 Å R-free 0.261 |
| 1FJS CRYSTAL STRUCTURE OF THE INHIBITOR ZK-807834 (CI-1031) COMPLEXED WITH FACTOR XA Deposited 2000-08-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：HEAVY CHAIN, CATALYTIC DOMAIN
Chain L
127–178（52 aa）
Fragment：LIGHT CHAIN, EPIDERMAL GROWTH FACTOR LIKE DOMAIN
|
Not recorded | CA CALCIUM ION × 1 CL CHLORIDE ION × 1 Z34 N-[2-[5-[AMINO(IMINO)METHYL]-2-HYDROXYPHENOXY]-3,5-DIFLUORO-6-[3-(4,5-DIHYDRO-1-METHYL-1H-IMIDAZOL-2-YL)PHENOXY]PYRIDIN-4-YL]-N-METHYLGLYCINE × 1 GOL GLYCEROL × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；295 K；Drop;
2 microliter,
12 mg/ml Factor Xa,
50 mM Tris pH 8.0, 75 mM NaCl
+ 2 microlter reservoir:
Reservoir;
15-21% PEG-1500 and 10mM CaCl2, VAPOR DIFFUSION, temperature 295K
|
Resolution 1.92 Å R-free 0.256 |
| 1G2L FACTOR XA INHIBITOR COMPLEX Deposited 2000-10-20 | Different construct Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–469（235 aa）
Fragment：CATALYTIC DOMAIN
Chain B
86–179（94 aa）
Fragment：DES-GLA FRAGMENT
|
Not recorded | CA CALCIUM ION × 1 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 1.90 Å R-free 0.272 |
| 1G2M FACTOR XA INHIBITOR COMPLEX Deposited 2000-10-20 | Different construct Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–469（235 aa）
Fragment：CATALYTIC DOMAIN
Chain B
86–179（94 aa）
Fragment：DES-GLA FRAGMENT
|
Not recorded | CA CALCIUM ION × 1 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 3.02 Å R-free 0.278 |
| 1HCG STRUCTURE OF HUMAN DES(1-45) FACTOR XA AT 2.2 ANGSTROMS RESOLUTION Deposited 1993-05-05 | Different construct Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–475（241 aa）
Chain B
129–179（51 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.20 Å |
| 1IOE Human coagulation factor Xa in complex with M55532 Deposited 2001-03-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–469（235 aa）
Fragment：HEAVY CHAIN, CATALYTIC DOMAIN (RESIDUES 235-469)
Chain L
84–179（96 aa）
Fragment：LIGHT CHAIN, EPIDERMAL GROWTH FACTOR LIKE DOMAIN (RESIDUES 84-179)
|
Not recorded | CA CALCIUM ION × 1 XMA (-)-7-[(6-CHLORO-2-NAPHTHALENYL)SULFONYL]TETRAHYDRO-8A-(METHOXYMETHYL)-1'-(4-PYRIDINYL)-SPIRO[5H-OXAZOLO[3,2-A]PYRAZINE-2(3H),4'-PIPERIDIN]-5-ONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；PEG1500, CALCIUM CHLORIDE, M55532,TRIS-HCL, pH 7.20, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
|
Resolution 2.90 Å R-free 0.295 |
| 1IQE Human coagulation factor Xa in complex with M55590 Deposited 2001-07-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–469（235 aa）
Fragment：heavy chain, catalytic domain (residues 235-469)
Chain L
84–179（96 aa）
Fragment：light chain, epidermal growth factor like domain (residues 84-179)
|
Not recorded | CA CALCIUM ION × 1 XMB 4-[(2R)-3-[[(6-CHLORO-2-NAPHTHALENYL)SULFONYL]AMINO]-1-OXO-2-[[[1-(4-PYRIDINYL)-4-PIPERIDINYL]METHYL]AMINO]PROPYL]-THIOMORPHOLINE-1,1-DIOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；PEG1500, calcium chloride, M55590, tris-HCl, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.90 Å R-free 0.297 |
| 1IQF Human coagulation factor Xa in complex with M55165 Deposited 2001-07-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–469（235 aa）
Fragment：heavy chain, catalytic domain (residues 235-469)
Chain L
84–179（96 aa）
Fragment：light chain, epidermal growth factor like domain (residues 84-179)
|
Not recorded | CA CALCIUM ION × 1 XMD (2R)-4-[(6-CHLORO-2-NAPHTHALENYL)SULFONYL]-6-OXO-1-[[1-(4-PYRIDINYL)-4-PIPERIDINYL]METHYL]-2-PIPERAZINECARBOXYLIC ACID ETHYL ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；PEG1500, calcium chloride, M55165, tris-HCl, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 3.20 Å R-free 0.277 |
| 1IQG Human coagulation factor Xa in complex with M55159 Deposited 2001-07-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–469（235 aa）
Fragment：heavy chain, catalytic domain (residues 235-469)
Chain L
84–179（96 aa）
Fragment：light chain, epidermal growth factor like domain (residues 84-179)
|
Not recorded | CA CALCIUM ION × 1 XME 4-[(6-CHLORO-2-NAPHTHALENYL)SULFONYL]-1-[[4-HYDROXYIMINOMETHYL-1-(4-PYRIDINYL)-4-PIPERIDINYL]METHYL]PIPERAZINONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；PEG1500, calcium chloride, M55159, tris-HCl, pH 7.20, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.60 Å R-free 0.271 |
| 1IQH Human coagulation factor Xa in complex with M55143 Deposited 2001-07-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–469（235 aa）
Fragment：heavy chain, catalytic domain (residues 235-469)
Chain L
84–179（96 aa）
Fragment：light chain, epidermal growth factor like domain (residues 84-179)
|
Not recorded | CA CALCIUM ION × 1 XMF 4-[(6-CHLORO-2-NAPHTHALENYL)SULFONYL]-1-[[4-HYDROXYMETHYL-1-(4-PYRIDINYL)-4-PIPERIDINYL]METHYL]PIPERAZINONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；PEG1500, calcium chloride, M55143, tris-HCl, pH 7.20, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 3.00 Å R-free 0.286 |
| 1IQI Human coagulation factor Xa in complex with M55125 Deposited 2001-07-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–469（235 aa）
Fragment：heavy chain, catalytic domain (residues 235-469)
Chain L
84–179（96 aa）
Fragment：light chain, epidermal growth factor like domain (residues 84-179)
|
Not recorded | CA CALCIUM ION × 1 XMG 4-[(6-CHLORO-2-NAPHTHALENYL)SULFONYL]-1-[[1-(4-PYRIDINYL)-4-PIPERIDINYL] METHYL]-2-PIPERAZINECARBOXYLIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；PEG1500, calcium chloride, M55125, tris-HCl, pH 7.20, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.90 Å R-free 0.290 |
| 1IQJ Human coagulation factor Xa in complex with M55124 Deposited 2001-07-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–469（235 aa）
Fragment：heavy chain, catalytic domain (residues 235-469)
Chain L
84–179（96 aa）
Fragment：light chain, epidermal growth factor like domain (residues 84-179)
|
Not recorded | CA CALCIUM ION × 1 XMH 4-[(6-CHLORO-2-NAPHTHALENYL)SULFONYL]-1-[[1-(4-PYRIDINYL)-4-PIPERIDINYL]METHYL]-2-PIPERAZINECARBOXYLIC ACID ETHYL ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；PEG1500, calcium chloride, M55124, tris-HCl, pH 7.20, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 3.00 Å R-free 0.293 |
| 1IQK Human coagulation factor Xa in complex with M55113 Deposited 2001-07-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–469（235 aa）
Fragment：heavy chain, catalytic domain (residues 235-469)
Chain L
84–179（96 aa）
Fragment：light chain, epidermal growth factor like domain (residues 84-179)
|
Not recorded | CA CALCIUM ION × 1 XMI 4-[(6-CHLORO-2-NAPHTHALENYL)SULFONYL]-1-[[1-(4-PYRIDINYL)-4-PIPERIDINYL]METHYL]PIPERAZINONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；PEG1500, calcium chloride, M55113, tris-HCl, pH 7.20, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 3.20 Å R-free 0.280 |
| 1IQL Human coagulation factor Xa in complex with M54476 Deposited 2001-07-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–469（235 aa）
Fragment：heavy chain, catalytic domain (residues 235-469)
Chain L
84–179（96 aa）
Fragment：light chain, epidermal growth factor like domain (residues 84-179)
|
Not recorded | CA CALCIUM ION × 1 XMJ 4-[[(1E)-2-(4-CHLOROPHENYL)ETHENYL]SULFONYL]-1-[[1-(4-PYRIDINYL)-4-PIPERIDINYL]METHYL]PIPERAZINONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；PEG1500, calcium chloride, M54476, tris-HCl, pH 7.20, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.304 |
| 1IQM Human coagulation factor Xa in complex with M54471 Deposited 2001-07-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–469（235 aa）
Fragment：heavy chain, catalytic domain (residues 235-469)
Chain L
84–179（96 aa）
Fragment：light chain, epidermal growth factor like domain (residues 84-179)
|
Not recorded | CA CALCIUM ION × 1 XMK 1-[[(1E)-2-(4-CHLOROPHENYL)ETHENYL]SULFONYL]-4-[[1-(4-PYRIDINYL)-4-PIPERIDINYL]METHYL]PIPERAZINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；PEG1500, calcium chloride, M54471, tris-HCl, pH 7.20, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.60 Å R-free 0.284 |
| 1IQN Human coagulation factor Xa in complex with M55192 Deposited 2001-07-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–469（235 aa）
Fragment：heavy chain, catalytic domain (residues 235-469)
Chain L
84–179（96 aa）
Fragment：light chain, epidermal growth factor like domain (residues 84-179)
|
Not recorded | CA CALCIUM ION × 1 XMC 4-[[4-[(6-CHLORO-2-NAPHTHALENYL)SULFONYL]-6-OXO-1-[[1-(4-PYRIDINYL)-4-PIPERIDINYL]METHYL]-2-PIPERAZINYL]CARBONYL]MORPHOLINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；PEG1500, calcium chloride, M55192, tris-HCl, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.60 Å R-free 0.254 |
| 1KSN Crystal Structure of Human Coagulation Factor XA Complexed with FXV673 Deposited 2002-01-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Fragment：ACTIVATED FACTOR XA, HEAVY CHAIN
Chain B
46–179（134 aa）
Fragment：FACTOR X LIGHT CHAIN
|
Not recorded | CA CALCIUM ION × 1 FXV METHYL-3-(4'-N-OXOPYRIDYLPHENOYL)-3-METHYL-2-(M-AMIDINOBENZYL)-PROPIONATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；292 K；18-20% PEG 600, 50MM MES-NAOH, 1MM RPR128515, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 2.10 Å |
| 1LPG CRYSTAL STRUCTURE OF FXA IN COMPLEX WITH 79. Deposited 2002-05-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
46–179（134 aa）
Fragment：light chain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；PEG600, MES, CaCl2, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 2.00 Å R-free 0.288 |
| 1LPG CRYSTAL STRUCTURE OF FXA IN COMPLEX WITH 79. Deposited 2002-05-08 | 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
235–488（254 aa）
|
Not recorded | CA CALCIUM ION × 1 IMA [4-({[5-BENZYLOXY-1-(3-CARBAMIMIDOYL-BENZYL)-1H-INDOLE-2-CARBONYL]-AMINO}-METHYL)-PHENYL]-TRIMETHYL-AMMONIUM × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；PEG600, MES, CaCl2, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 2.00 Å R-free 0.288 |
| 1LPK CRYSTAL STRUCTURE OF FXA IN COMPLEX WITH 125. Deposited 2002-05-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
46–179（134 aa）
Fragment：light chain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；PEG600, MES, CaCl2, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 2.20 Å R-free 0.280 |
| 1LPK CRYSTAL STRUCTURE OF FXA IN COMPLEX WITH 125. Deposited 2002-05-08 | 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
235–488（254 aa）
|
Not recorded | CA CALCIUM ION × 1 CBB 1-(3-CARBAMIMIDOYL-BENZYL)-1H-INDOLE-2-CARBOXYLIC ACID 3-CARBAMIMIDOYL-BENZYLESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；PEG600, MES, CaCl2, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 2.20 Å R-free 0.280 |
| 1LPZ CRYSTAL STRUCTURE OF FXA IN COMPLEX WITH 41. Deposited 2002-05-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
46–179（134 aa）
Fragment：light chain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；PEG600, MES, CaCl2, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 2.40 Å R-free 0.279 |
| 1LPZ CRYSTAL STRUCTURE OF FXA IN COMPLEX WITH 41. Deposited 2002-05-08 | 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
235–488（254 aa）
|
Not recorded | CA CALCIUM ION × 1 CMB 1-(3-carbamimidoylbenzyl)-N-(3,5-dichlorobenzyl)-4-methyl-1H-indole-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；PEG600, MES, CaCl2, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 2.40 Å R-free 0.279 |
| 1LQD CRYSTAL STRUCTURE OF FXA IN COMPLEX WITH 45. Deposited 2002-05-10 | 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
46–179（134 aa）
Fragment：light chain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；PEG600, MES, CaCl2, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 2.70 Å R-free 0.295 |
| 1LQD CRYSTAL STRUCTURE OF FXA IN COMPLEX WITH 45. Deposited 2002-05-10 | 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
235–488（254 aa）
|
Not recorded | CA CALCIUM ION × 1 CMI 1-(3-CARBAMIMIDOYL-BENZYL)-4-METHYL-1H-INDOLE-2-CARBOXYLIC ACID 3,5-DIMETHYL-BENZYLAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；PEG600, MES, CaCl2, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 2.70 Å R-free 0.295 |
| 1MQ5 Crystal Structure of 3-chloro-N-[4-chloro-2-[[(4-chlorophenyl)amino]carbonyl]phenyl]-4-[(4-methyl-1-piperazinyl)methyl]-2-thiophenecarboxamide Complexed with Human Factor Xa Deposited 2002-09-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–467（233 aa）
Fragment：CATALYTIC DOMAIN
Chain L
127–177（51 aa）
Fragment：EPIDERMAL GROWTH FACTOR LIKE DOMAIN 2
|
Not recorded | CA CALCIUM ION × 1 XLC 3-CHLORO-N-[4-CHLORO-2-[[(4-CHLOROPHENYL)AMINO]CARBONYL]PHENYL]-4-[(4-METHYL-1-PIPERAZINYL)METHYL]-2-THIOPHENECARBOXAMIDE × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；A THREE-FOLD EXCESS OF A
PROPRIETARY FACTOR XA INHIBITOR WITH PICOMOLAR AFFINITY WAS
ADDED TO THE DES-GLA-FACTOR XA. THIS INHIBITOR IS BASED
ON THE SAME TEMPLATE AS XLC IN 1MQ5. THE PROTEIN WAS THEN
CONCENTRATED TO 12-17 MG/ML. CRYSTALS WERE GROWN USING 2 UL
OF COMPLEX WITH 2 UL OF RESERVOIR CONTAINING 15-21% PEG1500
AND 10 MM CACL2. 30-40 UL SITTING DROPS CONTAINING
SATURATED INHIBITOR (5 MM) IN 21% PEG1500, 5 MM CACL2, 50
MM NACL, 50 MM TRIS PH 7.5 (CRYSTAL SOAKING SOLUTION)
WERE EQUILIBRATED OVER A 1 ML RESERVOIR CONTAINING THE
CRYSTAL SOAKING SOLUTION FOR 1 TO 2 DAYS. A SINGLE FACTOR
XA CRYSTAL WAS TRANSFERRED USING A MOUNTED CRYOLOOP INTO ONE
OF THESE SITTING DROPS AND ALLOWED TO SOAK FOR THREE OR MORE
Days. AFTER THE INITIAL SOAK, EACH CRYSTAL WAS THEN
TRANSFERRED TO AN UNUSED DROP AND ALLOWED TO SOAK FOR SECOND
PERIOD OF THREE OR MORE DAYS. pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.10 Å R-free 0.264 |
| 1MQ6 Crystal Structure of 3-chloro-N-[4-chloro-2-[[(5-chloro-2-pyridinyl)amino]carbonyl]-6-methoxyphenyl]-4-[[(4,5-dihydro-2-oxazolyl)methylamino]methyl]-2-thiophenecarboxamide Complexed with Human Factor Xa Deposited 2002-09-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–467（233 aa）
Fragment：CATALYTIC DOMAIN
Chain L
127–177（51 aa）
Fragment：EPIDERMAL GROWTH FACTOR LIKE DOMAIN 2
|
Not recorded | CA CALCIUM ION × 1 XLD 3-CHLORO-N-[4-CHLORO-2-[[(5-CHLORO-2-PYRIDINYL)AMINO]CARBONYL]-6-METHOXYPHENYL]-4-[[(4,5-DIHYDRO-2-OXAZOLYL)METHYLAMINO]METHYL]-2-THIOPHENECARBOXAMIDE × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；A THREE-FOLD EXCESS OF A PROPRIETARY FACTOR XA INHIBITOR WITH PICOMOLAR AFFINITY WAS
ADDED TO THE DES-GLA-FACTOR XA. THIS INHIBITOR IS BASED
ON THE SAME TEMPLATE AS XLD IN 1MQ6. THE PROTEIN WAS THEN
CONCENTRATED TO 12-17 MG/ML. CRYSTALS WERE GROWN USING 2 UL
OF COMPLEX WITH 2 UL OF RESERVOIR CONTAINING 15-21% PEG1500
AND 10 MM CACL2. 30-40 UL SITTING DROPS CONTAINING
SATURATED INHIBITOR (5 MM) IN 21% PEG1500, 5 MM CACL2, 20
MM NACL, 25 MM TRIS PH 7.5 (CRYSTAL SOAKING SOLUTION)
WERE EQUILIBRATED OVER A 1 ML RESERVOIR CONTAINING THE
CRYSTAL SOAKING SOLUTION FOR 1 TO 2 DAYS. A SINGLE FACTOR
XA CRYSTAL WAS TRANSFERRED USING A MOUNTED CRYOLOOP INTO ONE
OF THESE SITTING DROPS AND ALLOWED TO SOAK FOR THREE OR MORE
DAYS. AFTER THE INITIAL SOAK, EACH CRYSTAL WAS THEN
TRANSFERRED TO AN UNUSED DROP AND ALLOWED TO SOAK FOR SECOND
PERIOD OF THREE OR MORE DAYS. pH 7.50, VAPOR DIFFUSION, HANGING DROP,
temperature 293K
|
Resolution 2.10 Å R-free 0.268 |
| 1NFU CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR XA COMPLEXED WITH RPR132747 Deposited 2002-12-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Chain B
46–240（195 aa）
|
Not recorded | CA CALCIUM ION × 1 RRP 3-({4-[(6-CHLORO-1-BENZOTHIEN-2-YL)SULFONYL]-2-OXOPIPERAZIN-1-YL}METHYL)BENZENECARBOXIMIDAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；292 K；18-20% PEG 600, 50MM MES-NAOH,1MM RPR132747, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 2.05 Å |
| 1NFW CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR XA COMPLEXED WITH RPR209685 Deposited 2002-12-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Chain B
46–179（134 aa）
|
Not recorded | CA CALCIUM ION × 1 RRR 4-{[(E)-2-(5-CHLOROTHIEN-2-YL)VINYL]SULFONYL}-1-(1H-PYRROLO[3,2-C]PYRIDIN-2-YLMETHYL)PIPERAZIN-2-ONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；292 K；18-20% PEG 600, 50MM MES-NAOH,1MM RPR209685, pH 5.70 , VAPOR DIFFUSION, HANGING DROP, temperature 292 K
|
Resolution 2.10 Å |
| 1NFX CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR XA COMPLEXED WITH RPR208944 Deposited 2002-12-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Chain B
46–179（134 aa）
|
Not recorded | CA CALCIUM ION × 1 RDR 4-[(6-CHLORO-1-BENZOTHIEN-2-YL)SULFONYL]-1-{[1-(2-HYDROXYETHYL)-1H-PYRROLO[3,2-C]PYRIDIN-2-YL]METHYL}PIPERAZIN-2-ONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；292 K；18-20% PEG 600, 50MM MES-NAOH,1MM RPR208944, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 2.15 Å |
| 1NFY CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR XA COMPLEXED WITH RPR200095 Deposited 2002-12-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Chain B
46–179（134 aa）
|
Not recorded | CA CALCIUM ION × 1 RTR 4-({4-[(6-CHLORO-1-BENZOTHIEN-2-YL)SULFONYL]-2-OXOPIPERAZIN-1-YL}METHYL)BENZENECARBOXIMIDAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；292 K；18-20% PEG 600, 50MM MES-NAOH,1MM RPR200095, pH 5.70, VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 2.10 Å |
| 1P0S Crystal Structure of Blood Coagulation Factor Xa in Complex with Ecotin M84R Deposited 2003-04-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain H
235–488（254 aa）
Fragment：Factor Xa Heavy Chain
Chain L
41–178（138 aa）
Fragment：Factor Xa Light Chain
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 8 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.1；298 K；PEG 3350, sodium potassium tartrate, sodium chloride, magnesium chloride, glycerol, MPD , pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.80 Å R-free 0.234 |
| 1V3X Factor Xa in complex with the inhibitor 1-[6-methyl-4,5,6,7-tetrahydrothiazolo(5,4-c)pyridin-2-yl] carbonyl-2-carbamoyl-4-(6-chloronaphth-2-ylsulphonyl)piperazine Deposited 2003-11-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–467（233 aa）
Fragment：Residues 16-243
Chain B
127–178（52 aa）
Fragment：Residues 87-138
|
Not recorded | CA CALCIUM ION × 2 D76 (2R)-4-[(6-CHLORO-2-NAPHTHYL)SULFONYL]-1-[(5-METHYL-4,5,6,7-TETRAHYDRO[1,3]THIAZOLO[5,4-C]PYRIDIN-2-YL)CARBONYL]PIPERAZ INE-2-CARBOXAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, macro-seeding, Soaking；pH 5；293 K；PEG6000, sodium acetate, Malate imidazole, Calcium chloride, pH 5.00, vapor diffusion, macro-seeding, Soaking, temperature 293K
|
Resolution 2.20 Å R-free 0.233 |
| 1WU1 Factor Xa in complex with the inhibitor 4-[(5-chloroindol-2-yl)sulfonyl]-2-(2-methylpropyl)-1-[[5-(pyridin-4-yl) pyrimidin-2-yl]carbonyl]piperazine Deposited 2004-11-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–467（233 aa）
Fragment：RESIDUES 16-243
Chain B
85–179（95 aa）
Fragment：RESIDUES 85-138
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CA CALCIUM ION × 2 D91 5-CHLORO-2-({3-ISOBUTYL-4-[(5-PYRIDIN-4-YLPYRIMIDIN-2-YL)CARBONYL]PIPERAZIN-1-YL}SULFONYL)-1H-INDOLE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；PEG6000, NaAcetate, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.30 Å R-free 0.235 |
| 1XKA FACTOR XA COMPLEXED WITH A SYNTHETIC INHIBITOR FX-2212A,(2S)-(3'-AMIDINO-3-BIPHENYLYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID Deposited 1998-03-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
235–469（235 aa）
Fragment：PROTEOLYTIC CLEAVAGE PRODUCT, GLA DOMAIN
Chain L
85–179（95 aa）
Fragment：PROTEOLYTIC CLEAVAGE PRODUCT, GLA DOMAIN
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CA CALCIUM ION × 1 4PP (2S)-(3'-AMIDINO-3-BIPHENYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；pH 5.5
|
Resolution 2.30 Å R-free 0.287 |
| 1XKB FACTOR XA COMPLEXED WITH A SYNTHETIC INHIBITOR FX-2212A,(2S)-(3'-AMIDINO-3-BIPHENYLYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID Deposited 1998-03-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
85–179（95 aa）
Fragment：PROTEOLYTIC CLEAVAGE PRODUCT, GLA DOMAIN
Chain C
235–469（235 aa）
Fragment：PROTEOLYTIC CLEAVAGE PRODUCT, GLA DOMAIN
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CA CALCIUM ION × 2 4PP (2S)-(3'-AMIDINO-3-BIPHENYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；pH 6.0
|
Resolution 2.40 Å R-free 0.294 |
| 1XKB FACTOR XA COMPLEXED WITH A SYNTHETIC INHIBITOR FX-2212A,(2S)-(3'-AMIDINO-3-BIPHENYLYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID Deposited 1998-03-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
85–179（95 aa）
Fragment：PROTEOLYTIC CLEAVAGE PRODUCT, GLA DOMAIN
Chain D
235–469（235 aa）
Fragment：PROTEOLYTIC CLEAVAGE PRODUCT, GLA DOMAIN
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CA CALCIUM ION × 1 4PP (2S)-(3'-AMIDINO-3-BIPHENYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；pH 6.0
|
Resolution 2.40 Å R-free 0.294 |
| 1XKB FACTOR XA COMPLEXED WITH A SYNTHETIC INHIBITOR FX-2212A,(2S)-(3'-AMIDINO-3-BIPHENYLYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID Deposited 1998-03-19 | 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
85–179（95 aa）
Fragment：PROTEOLYTIC CLEAVAGE PRODUCT, GLA DOMAIN
Chain B
85–179（95 aa）
Fragment：PROTEOLYTIC CLEAVAGE PRODUCT, GLA DOMAIN
Chain C
235–469（235 aa）
Fragment：PROTEOLYTIC CLEAVAGE PRODUCT, GLA DOMAIN
Chain D
235–469（235 aa）
Fragment：PROTEOLYTIC CLEAVAGE PRODUCT, GLA DOMAIN
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CA CALCIUM ION × 3 4PP (2S)-(3'-AMIDINO-3-BIPHENYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；pH 6.0
|
Resolution 2.40 Å R-free 0.294 |
| 1XKB FACTOR XA COMPLEXED WITH A SYNTHETIC INHIBITOR FX-2212A,(2S)-(3'-AMIDINO-3-BIPHENYLYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID Deposited 1998-03-19 | 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 A
85–179（95 aa）
Fragment：PROTEOLYTIC CLEAVAGE PRODUCT, GLA DOMAIN
Chain B
85–179（95 aa）
Fragment：PROTEOLYTIC CLEAVAGE PRODUCT, GLA DOMAIN
Chain C
235–469（235 aa）
Fragment：PROTEOLYTIC CLEAVAGE PRODUCT, GLA DOMAIN
Chain D
235–469（235 aa）
Fragment：PROTEOLYTIC CLEAVAGE PRODUCT, GLA DOMAIN
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CA CALCIUM ION × 3 4PP (2S)-(3'-AMIDINO-3-BIPHENYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；pH 6.0
|
Resolution 2.40 Å R-free 0.294 |
| 1Z6E Factor XA in complex with the inhibitor 1-(3'-amino-1,2-benzisoxazol-5'-yl)-n-(4-(2'-((dimethylamino)methyl)-1h-imidazol-1-yl)-2-fluorophenyl)-3-(trifluoromethyl)-1h-pyrazole-5-carboxamide (razaxaban; DPC906; BMS-561389) Deposited 2005-03-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：UNP residues 235-468
Chain L
127–178（52 aa）
Fragment：UNP residues 127-178
|
Not recorded | IK8 1-(3-AMINO-1,2-BENZISOXAZOL-5-YL)-N-(4-{2-[(DIMETHYLAMINO)METHYL]-1H-IMIDAZOL-1-YL}-2-FLUOROPHENYL)-3-(TRIFLUOROMETHYL) -1H-PYRAZOLE-5-CARBOXAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；200 mM Sodium Acetate, pH 5.5, 18% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.80 Å R-free 0.260 |
| 2BMG Crystal structure of factor Xa in complex with 50 Deposited 2005-03-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
126–178（53 aa）
Fragment：LIGHT CHAIN, RESIDUES 126-178
Chain B
235–468（234 aa）
Fragment：HEAVY CHAIN, RESIDUES 235-468
|
Not recorded | CA CALCIUM ION × 1 I1H 3-[2-(2,4-DICHLOROPHENYL)ETHOXY]-4-METHOXY-N-[(1-PYRIDIN-4-YLPIPERIDIN-4-YL)METHYL]BENZAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；PEG600, MES, CACL2, PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K
|
Resolution 2.70 Å R-free 0.277 |
| 2BOH Crystal structure of factor Xa in complex with compound "1" Deposited 2005-04-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
126–234（109 aa）
Fragment：LIGHT CHAIN, RESIDUES 126-234
Chain B
235–488（254 aa）
Fragment：LIGHT CHAIN, RESIDUES 235-488
|
Not recorded | CA CALCIUM ION × 1 IIA 1-{[5-(5-CHLORO-2-THIENYL)ISOXAZOL-3-YL]METHYL}-N-(1-ISOPROPYLPIPERIDIN-4-YL)-1H-INDOLE-2-CARBOXAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；PEG600, MES, CACL2, PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0 K
|
Resolution 2.20 Å R-free 0.253 |
| 2BOK Factor Xa - cation Deposited 2005-04-12 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–475（241 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 234-475
Chain L
126–180（55 aa）
Fragment：EGF2 DOMAIN, RESIDUES 126-180
|
Mutation：YES | 784 [AMINO (4-{(3AS,4R,8AS,8BR)-1,3-DIOXO-2- [3-(TRIMETHYLAMMONIO) PROPYL]DECAHYDROPYRROLO[3,4-A] PYRROLIZIN-4-YL}PHENYL) METHYLENE]AMMONIUM × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；pH 5.50
|
Resolution 1.64 Å R-free 0.237 |
| 2BQ6 Crystal structure of factor Xa in complex with 21 Deposited 2005-04-27 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
126–177（52 aa）
Fragment：DES-GLA LIGHT CHAIN, RESIDUES 126-177
Chain B
220–368（149 aa）
Fragment：HEAVY CHAIN, RESIDUES 220-468
Chain B
369–441（73 aa）
Fragment：HEAVY CHAIN, RESIDUES 220-468
Chain B
442–468（27 aa）
Fragment：HEAVY CHAIN, RESIDUES 220-468
|
Not recorded | CA CALCIUM ION × 1 IIB 1-{[5-(5-CHLORO-2-THIENYL)ISOXAZOL-3-YL]METHYL}-3-CYANO-N-(1-ISOPROPYLPIPERIDIN-4-YL)-7-METHYL-1H-INDOLE-2-CARBOXAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；PEG600, MES, CACL2, PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K
|
Resolution 3.00 Å R-free 0.298 |
| 2BQ7 Crystal structure of factor Xa in complex with 43 Deposited 2005-04-27 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
126–177（52 aa）
Fragment：DES-GLA LIGHT CHAIN, RESIDUES 126-177
Chain B
220–368（149 aa）
Fragment：HEAVY CHAIN, RESIDUES 220-468
Chain B
369–441（73 aa）
Fragment：HEAVY CHAIN, RESIDUES 220-468
Chain B
342–468（127 aa）
Fragment：HEAVY CHAIN, RESIDUES 220-468
|
Not recorded | IID N-(1-ISOPROPYLPIPERIDIN-4-YL)-1-(3-METHOXYBENZYL)-1H-INDOLE-2-CARBOXAMIDE × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；PEG600, MES, CACL2, PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0 K
|
Resolution 2.20 Å R-free 0.272 |
| 2BQW CRYSTAL STRUCTURE OF FACTOR XA IN COMPLEX WITH COMPOUND 45 Deposited 2005-04-28 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
126–177（52 aa）
Fragment：DES-GLA LIGHT CHAIN, RESIDUES 126-177
Chain B
220–368（149 aa）
Fragment：HEAVY CHAIN, RESIDUES 220-468
Chain B
369–441（73 aa）
Fragment：HEAVY CHAIN, RESIDUES 220-468
Chain B
442–468（27 aa）
Fragment：HEAVY CHAIN, RESIDUES 220-468
|
Not recorded | CA CALCIUM ION × 1 IIE 1-{2-[(4-CHLOROPHENYL)AMINO]-2-OXOETHYL}-N-(1-ISOPROPYLPIPERIDIN-4-YL)-1H-INDOLE-2-CARBOXAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；PEG600, MES, CACL2, PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0 K
|
Resolution 2.95 Å R-free 0.261 |
| 2CJI Crystal structure of a Human Factor Xa inhibitor complex Deposited 2006-04-03 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–368（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain A
369–441（73 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain A
442–488（47 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
Not recorded | CA CALCIUM ION × 1 GSK 6-CHLORO-N-{(3S)-1-[(1S)-1-METHYL-2-(4-MORPHOLINYL)-2-OXO ETHYL]-2-OXO-3-PYRROLIDINYL}-2-NAPHTHALENESULFONAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.75；18% PEG 6K, 100MM MES PH5.75, 10MM CACL2
|
Resolution 2.10 Å R-free 0.242 |
| 2D1J Factor Xa in complex with the inhibitor 2-[[4-[(5-chloroindol-2-yl)sulfonyl]piperazin-1-yl] carbonyl]thieno[3,2-b]pyridine n-oxide Deposited 2005-08-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–467（233 aa）
Fragment：RESIDUES 16-243
Chain B
125–178（54 aa）
Fragment：RESIDUES 85-138
|
Not recorded | CA CALCIUM ION × 2 D01 2-({4-[(5-CHLORO-1H-INDOL-2-YL)SULFONYL]PIPERAZIN-1-YL}CARBONYL)THIENO[3,2-B]PYRIDINE 4-OXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SEEDING；pH 5；293 K；pH 5.00, VAPOR DIFFUSION, SEEDING, temperature 293K
|
Resolution 2.20 Å R-free 0.232 |
| 2EI6 FACTOR XA IN COMPLEX WITH THE INHIBITOR (-)-cis-N1-[(5-Chloroindol-2-yl)carbonyl]-N2-[(5-methyl-4,5,6,7-tetrahydrothiazolo[5,4-c]pyridin-2-yl)carbonyl]-1,2-cyclohexanediamine Deposited 2007-03-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–467（233 aa）
Fragment：RESIDUES 16-243
Chain B
125–178（54 aa）
Fragment：RESIDUES 85-138
|
Not recorded | CA CALCIUM ION × 2 D92 N-((1R,2S)-2-(5-CHLORO-1H-INDOLE-2-CARBOXAMIDO)CYCLOHEXYL)-5-METHYL-4,5,6,7-TETRAHYDROTHIAZOLO[5,4-C]PYRIDINE-2-CARBOXAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, hanging drop, seeding；pH 5；293 K；pH 5.00, vapor diffusion, hanging drop, seeding, temperature 293K
|
Resolution 2.30 Å R-free 0.262 |
| 2EI7 FACTOR XA IN COMPLEX WITH THE INHIBITOR trans-N1-[(5-Chloroindol-2-yl)carbonyl]-N2-[(5-methyl-4,5,6,7-tetrahydrothiazolo[5,4-c]pyridin-2-yl)carbonyl]-1,2-cyclohexanediamine Deposited 2007-03-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–467（233 aa）
Fragment：RESIDUES 16-243
Chain B
125–178（54 aa）
Fragment：RESIDUES 85-138
|
Not recorded | CA CALCIUM ION × 2 D93 N-((1R,2R)-2-(5-CHLORO-1H-INDOLE-2-CARBOXAMIDO)CYCLOHEXYL)-5-METHYL-4,5,6,7-TETRAHYDROTHIAZOLO[5,4-C]PYRIDINE-2-CARBOXAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, hanging drop, seeding；pH 5；293 K；compound introduced with soaking method at pH 7, pH 5.00, vapor diffusion, hanging drop, seeding, temperature 293K
|
Resolution 2.30 Å R-free 0.273 |
| 2EI8 FACTOR XA IN COMPLEX WITH THE INHIBITOR (1S,2R,4S)-N1-[(5-chloroindol-2-yl)carbonyl]-4-(N,N-dimethylcarbamoyl)-N2-[(5-methyl-4,5,6,7-tetrahydrothiazolo[5,4-c]pyridin-2-yl)carbonyl]-1,2-cyclohexanediamine Deposited 2007-03-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–467（233 aa）
Fragment：RESIDUES 16-243
Chain B
125–178（54 aa）
Fragment：RESIDUES 85-138
|
Not recorded | CA CALCIUM ION × 2 DT8 N-((1R,2S,5S)-2-(5-CHLORO-1H-INDOLE-2-CARBOXAMIDO)-5-(DIMETHYLCARBAMOYL)CYCLOHEXYL)-5-METHYL-4,5,6,7-TETRAHYDROTHIAZOLO[5,4-C]PYRIDINE-2-CARBOXAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
vapor diffusion, hanging drop, seeding；pH 5；293 K；soaking method at pH 7, pH 5.00, vapor diffusion, hanging drop, seeding, temperature 293K
|
Resolution 2.10 Å R-free 0.250 |
| 2FZZ Factor Xa in complex with the inhibitor 1-(3-amino-1,2-benzisoxazol-5-yl)-6-(2'-(((3r)-3-hydroxy-1-pyrrolidinyl)methyl)-4-biphenylyl)-3-(trifluoromethyl)-1,4,5,6-tetrahydro-7h-pyrazolo[3,4-c]pyridin-7-one Deposited 2006-02-10 | Different construct Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：Coagulation Factor X, Heavy Chain
Chain L
127–178（52 aa）
Fragment：Coagulation Factor X, Light Chain
|
Not recorded | 5QC 1-(3-AMINO-1,2-BENZISOXAZOL-5-YL)-6-(2'-{[(3R)-3-HYDROXYPYRROLIDIN-1-YL]METHYL}BIPHENYL-4-YL)-3-(TRIFLUOROMETHYL)-1,4,5,6-TETRAHYDRO-7H-PYRAZOLO[3,4-C]PYRIDIN-7-ONE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.20 Å R-free 0.294 |
| 2G00 Factor Xa in complex with the inhibitor 3-(6-(2'-((dimethylamino)methyl)-4-biphenylyl)-7-oxo-3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-c]pyridin-1-yl)benzamide Deposited 2006-02-10 | Different construct Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：Coagulation Factor X, Heavy Chain
Chain L
127–178（52 aa）
Fragment：Coagulation Factor X, Light Chain
|
Not recorded | 4QC 3-[6-{2'-[(DIMETHYLAMINO)METHYL]BIPHENYL-4-YL}-7-OXO-3-(TRIFLUOROMETHYL)-4,5,6,7-TETRAHYDRO-1H-PYRAZOLO[3,4-C]PYRIDIN-1-YL]BENZAMIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.10 Å R-free 0.284 |
| 2GD4 Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex Deposited 2006-03-15 | 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
235–475（241 aa）
Fragment：Residues 235-475
Chain L
126–182（57 aa）
Fragment：Residues 126-182
|
Mutation：S195A | CA CALCIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；20% PEG 3350, 200mM Calcium Acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K
|
Resolution 3.30 Å R-free 0.298 |
| 2GD4 Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex Deposited 2006-03-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
126–182（57 aa）
Fragment：Residues 126-182
Chain B
235–475（241 aa）
Fragment：Residues 235-475
|
Mutation：S195A | CA CALCIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；20% PEG 3350, 200mM Calcium Acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K
|
Resolution 3.30 Å R-free 0.298 |
| 2H9E Crystal Structure of FXa/selectide/NAPC2 ternary complex Deposited 2006-06-09 | 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
235–467（233 aa）
Fragment：catalytic domain
Chain L
86–234（149 aa）
Fragment：EGF-like 1 domain
|
Not recorded | PO4 PHOSPHATE ION × 6 ACT ACETATE ION × 3 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；peg 8000, potassium dihydrogen phosphate, acetate ion, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.20 Å R-free 0.268 |
| 2J2U CRYSTAL STRUCTURE OF A HUMAN FACTOR XA INHIBITOR COMPLEX Deposited 2006-08-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
Not recorded | GSQ 5-CHLORO-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-5-CHLORO-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-SULFONAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.85；18% PEG6K, 50MM MES PH 5.85, 5MM CACL2, 50MM NACL
|
Resolution 1.90 Å R-free 0.236 |
| 2J34 CRYSTAL STRUCTURE OF A HUMAN FACTOR XA INHIBITOR COMPLEX Deposited 2006-08-18 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–368（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain A
369–441（73 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain A
442–488（47 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
Not recorded | GS6 6-CHLORO-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-OXOETHYL]-2-OXOPYRROLIDIN-3-YL}-1-BENZOTHIOPHENE-2-SULFONAMIDE × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.85；18% PEG6K, 50MM MES PH 5.85, 5MM CACL2, 50MM NACL
|
Resolution 2.01 Å R-free 0.220 |
| 2J38 CRYSTAL STRUCTURE OF A HUMAN FACTOR XA INHIBITOR COMPLEX Deposited 2006-08-18 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–368（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain A
369–441（73 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain A
442–488（47 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
Not recorded | GS5 5-CHLORO-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-OXOETHYL]-2-OXOPYRROLIDIN-3-YL}-1-BENZOTHIOPHENE-2-SULFONAMIDE × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.85；16% PEG6K, 50MM MES PH5.85, 5MM CACL2, 50MM NACL
|
Resolution 2.10 Å R-free 0.302 |
| 2J4I CRYSTAL STRUCTURE OF A HUMAN FACTOR XA INHIBITOR COMPLEX Deposited 2006-08-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
Not recorded | GSJ 1-PYRROLIDINEACETAMIDE, 3-[[(6-CHLORO-2-NAPHTHALENYL)SULFONYL]AMINO]-ALPHA-METHYL-N-(1-METHYLETHYL)-N-[2-[(METHYLSULFONYL)AMINO]ETHYL]-2-OXO-, (ALPHAS,3S)- × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.85；18% PEG6K, 50MM MES PH 5.85, 5MM CACL2, 50MM NACL
|
Resolution 1.80 Å R-free 0.234 |
| 2J94 CRYSTAL STRUCTURE OF A HUMAN FACTOR XA INHIBITOR COMPLEX Deposited 2006-11-02 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–368（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain A
369–441（73 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain A
442–488（47 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
Not recorded | G15 5-(5-CHLORO-2-THIENYL)-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-OXOETHYL]-2-OXOPYRROLIDIN-3-YL}-1H-1,2,4-TRIAZOLE-3-SULFONAMIDE × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.75；18% PEG6K, 50MM MES PH 5.85, 5MM CACL2, 50MM NACL
|
Resolution 2.10 Å R-free 0.233 |
| 2J95 CRYSTAL STRUCTURE OF A HUMAN FACTOR XA INHIBITOR COMPLEX Deposited 2006-11-02 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–368（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain A
369–441（73 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain A
442–488（47 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
Not recorded | GSX 5'-CHLORO-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-OXOETHYL]-2-OXOPYRROLIDIN-3-YL}-2,2'-BITHIOPHENE-5-SULFONAMIDE × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.85；18% PEG 6K, 100MM MES PH5.75, 10MM CACL2, pH 5.85
|
Resolution 2.01 Å R-free 0.242 |
| 2JKH Factor Xa - cation inhibitor complex Deposited 2008-08-28 | Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–475（241 aa）
Fragment：CATALYTIC, RESIDUES 235-475
Chain L
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Mutation：YES | BI7 3-[(3~{a}~{S},4~{R},8~{a}~{S},8~{b}~{R})-4-[5-(5-chloranylthiophen-2-yl)-1,2-oxazol-3-yl]-1,3-bis(oxidanylidene)-4,6,7,8,8~{a},8~{b}-hexahydro-3~{a}~{H}-pyrrolo[3,4-a]pyrrolizin-2-yl]propyl-trimethyl-azanium × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.25 Å R-free 0.221 |
| 2JKH Factor Xa - cation inhibitor complex Deposited 2008-08-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
235–475（241 aa）
Fragment：CATALYTIC, RESIDUES 235-475
|
Mutation：YES | BI7 3-[(3~{a}~{S},4~{R},8~{a}~{S},8~{b}~{R})-4-[5-(5-chloranylthiophen-2-yl)-1,2-oxazol-3-yl]-1,3-bis(oxidanylidene)-4,6,7,8,8~{a},8~{b}-hexahydro-3~{a}~{H}-pyrrolo[3,4-a]pyrrolizin-2-yl]propyl-trimethyl-azanium × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.25 Å R-free 0.221 |
| 2JKH Factor Xa - cation inhibitor complex Deposited 2008-08-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain L
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.25 Å R-free 0.221 |
| 2P16 Factor Xa in Complex with the Inhibitor APIXABAN (BMS-562247) AKA 1-(4-METHOXYPHENYL)-7-OXO-6-(4-(2-OXO-1-PIPERIDINYL)PHENYL)-4,5,6,7-TETRAHYDRO-1H-PYRAZOLO[3, 4-C]PYRIDINE-3-CARBOXAMIDE Deposited 2007-03-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：Coagulation Factor X, Heavy Chain
Chain L
127–178（52 aa）
Fragment：Coagulation Factor X, Light Chain
|
Not recorded | CA CALCIUM ION × 1 GG2 1-(4-METHOXYPHENYL)-7-OXO-6-[4-(2-OXOPIPERIDIN-1-YL)PHENYL]-4,5,6,7-TETRAHYDRO-1H-PYRAZOLO[3,4-C]PYRIDINE-3-CARBOXAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；277 K；200 mM Sodium Acetate, 18% PEG6000, vapor diffusion, hanging drop, temperature 277K, pH 5.5
|
Resolution 2.30 Å R-free 0.277 |
| 2P3F Crystal structure of the factor Xa/NAP5 complex Deposited 2007-03-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
235–469（235 aa）
Fragment：Activated factor Xa heavy chain domain
Chain L
125–178（54 aa）
Fragment：EGF-like 2 domain
|
Not recorded | NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；298 K；Peg400, sodium citrate, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.10 Å R-free 0.280 |
| 2P3T Crystal structure of human factor XA complexed with 3-Chloro-4-(2-methylamino-imidazol-1-ylmethyl)-thiophene-2-carboxylic acid [4-chloro-2-(5-chloro-pyridin-2-ylcarbamoyl)-6-methoxy-phenyl]-amide Deposited 2007-03-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
127–178（52 aa）
Fragment：EGF-like 2 domain
Chain B
235–467（233 aa）
Fragment：CATALYTIC DOMAIN
|
Not recorded | CA CALCIUM ION × 1 CL CHLORIDE ION × 1 993 3-CHLORO-4-(2-METHYLAMINO-IMIDAZOL-1-YLMETHYL)-THIOPHENE-2-CARBOXYLIC ACID [4-CHLORO-2-(5-CHLORO-PYRIDIN-2-YLCARBAMOYL)-6-METHOXY-PHENYL]-AMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；A three-fold excess of the inhibitor was added to the DES-GLA-FACTOR XA. the protein was then concentrated to 12-17 MG/ML. Crystals were grown using 2 UL of complex with 2 UL of reservoir containing 15-21% PEG1500 and 10 MM CACL2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.92 Å R-free 0.219 |
| 2P3U Crystal structure of human factor XA complexed with 3-chloro-N-(4-chloro-2-{[(5-chloropyridin-2-yl)amino]carbonyl}-6-methoxyphenyl)-4-[(1-methyl-1H-imidazol-2-yl)methyl]thiophene-2-carboxamide {Pfizer 320663} Deposited 2007-03-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
127–178（52 aa）
Fragment：EGF-like 2 domain
Chain B
235–467（233 aa）
Fragment：CATALYTIC DOMAIN
|
Not recorded | CA CALCIUM ION × 2 663 3-CHLORO-N-(4-CHLORO-2-{[(5-CHLOROPYRIDIN-2-YL)AMINO]CARBONYL}-6-METHOXYPHENYL)-4-[(1-METHYL-1H-IMIDAZOL-2-YL)METHYL]THIOPHENE-2-CARBOXAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 7.5；295 K；A THREE-FOLD EXCESS OF 3-Chloro-4-(2-methylamino-imidazol-1-ylmethyl)-thiophene-2-carboxylic acid [4-chloro-2-(5-chloro-pyridin-2-ylcarbamoyl)-6-methoxy-phenyl]-amide WAS ADDED TO THE DES-GLA-FACTOR XA. THE PROTEIN WAS THEN CONCENTRATED TO 12-17 MG/ML. CRYSTALS WERE GROWN USING 2 UL OF COMPLEX WITH 2 UL OF RESERVOIR CONTAINING 15-21% PEG1500 AND 10 MM CACL2. 30-40 UL SITTING DROPS CONTAINING SATURATED INHIBITOR (5 MM) IN 21% PEG1500, 5 MM CACL2, 20 MM NACL, 25 MM TRIS PH 7.5 (CRYSTAL SOAKING SOLUTION) WERE EQUILIBRATED OVER A 1 ML RESERVOIR CONTAINING THE CRYSTAL SOAKING SOLUTION FOR 1 TO 2 DAYS. A SINGLE FACTOR XA CRYSTAL WAS TRANSFERRED USING A MOUNTED CRYOLOOP INTO ONE OF THESE SITTING DROPS AND ALLOWED TO SOAK FOR THREE OR MORE DAYS, EVAPORATION, temperature 295K
|
Resolution 1.62 Å R-free 0.210 |
| 2P93 Factor xa in complex with the inhibitor 5-chloro-N-(2-(4-(2-oxopyridin-1(2H)-yl)benzamido)ethyl)thiophene-2-carboxamide Deposited 2007-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：Residues 16-243
Chain L
127–178（52 aa）
Fragment：Residues 87-138
|
Not recorded | ME1 5-CHLORO-N-(2-(4-(2-OXOPYRIDIN-1(2H)-YL)BENZAMIDO)ETHYL)THIOPHENE-2-CARBOXAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；200 mM Sodium Acetate, pH 5.5, 18% PEG6000, vapor diffusion, hanging drop, temperature 277K
|
Resolution 1.90 Å R-free 0.307 |
| 2P94 Factor xa in complex with the inhibitor 3-chloro-N-((1R,2S)-2-(4-(2-oxopyridin-1(2H)-yl)benzamido)cyclohexyl)-1H-indole-6-carboxamide Deposited 2007-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：Residues 16-244
Chain L
127–178（52 aa）
Fragment：Residues 87-138
|
Not recorded | ME4 3-CHLORO-N-((1R,2S) -2-(4-(2-OXOPYRIDIN-1(2H)-YL)BENZAMIDO)CYCLOHEXYL)-1H-INDOLE-6-CARBOXAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；200 mM Sodium Acetate, pH 5.5, 18% PEG6000, vapor diffusion, hanging drop, temperature 277K
|
Resolution 1.80 Å R-free 0.330 |
| 2P95 Factor xa in complex with the inhibitor 5-chloro-N-((1R,2S)-2-(4-(2-oxopyridin-1(2H)-YL)benzamido) cyclopentyl)thiophene-2-carboxamide Deposited 2007-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：Residues 16-244
Chain L
127–178（52 aa）
Fragment：Residues 87-138
|
Not recorded | ME5 5-CHLORO-N-((1R,2S)-2-(4-(2-OXOPYRIDIN-1(2H)-YL)BENZAMIDO) CYCLOPENTYL)THIOPHENE-2-CARBOXAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；200 mM Sodium Acetate, pH 5.5, 18% PEG6000, vapor diffusion, hanging drop, temperature 277K
|
Resolution 2.20 Å R-free 0.271 |
| 2PHB An Orally Efficacious Factor Xa Inhibitor Deposited 2007-04-10 | Different construct Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：heavy chain
Chain B
128–178（51 aa）
Fragment：light chain
|
Not recorded | CA CALCIUM ION × 1 230 (2R,4R)-N~1~-(4-CHLOROPHENYL)-N~2~-[2-FLUORO-4-(2-OXOPYRIDIN-1(2H)-YL)PHENYL]-4-METHOXYPYRROLIDINE-1,2-DICARBOXAMIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å R-free 0.296 |
| 2Q1J The discovery of glycine and related amino acid-based factor xa inhibitors Deposited 2007-05-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Chain B
128–178（51 aa）
Fragment：Residues 128-178
|
Not recorded | CA CALCIUM ION × 1 FXI 1-(butyl{[(4-chlorophenyl)amino]carbonyl}amino)-N-[3-fluoro-2'-(methylsulfonyl)biphenyl-4-yl]cyclopropanecarboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.9；25% PEG 600, 0.3 M NACL, 0.1 M MES, PH 5.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K, pH 5.90
|
Resolution 1.90 Å R-free 0.272 |
| 2RA0 X-ray Structure of FXa in complex with 7-fluoroindazole Deposited 2007-09-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：heavy chain, UNP residues 235-468
Chain L
128–178（51 aa）
Fragment：light chain, UNP residues 128-178
|
Mutation：L88V | JNJ 1-(3-amino-1,2-benzisoxazol-5-yl)-6-(4-{2-[(dimethylamino)methyl]-1H-imidazol-1-yl}-2-fluorophenyl)-7-fluoro-1H-indazole-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；20%Peg 3350, 10mM CaCl2, 0.1M Tris-maleate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.30 Å R-free 0.314 |
| 2UWL Selective and Dual Action Orally Active Inhibitors of Thrombin and Factor Xa Deposited 2007-03-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
Not recorded | 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 5.75；18% PEG6K, 50MM HEPES PH5.75, 10MM CACL2, 150MM NACL
|
Resolution 1.90 Å R-free 0.238 |
| 2UWO Selective and Dual Action Orally Active Inhibitors of Thrombin and Factor Xa Deposited 2007-03-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
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 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.75；18% PEG6K, 50MM MES PH5.75, 10MM CACL2, 150MM NACL
|
Resolution 1.75 Å R-free 0.254 |
| 2UWP Factor Xa inhibitor complex Deposited 2007-03-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
Not recorded | 894 2-(5-CHLORO-2-THIENYL)-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-OXOETHYL]-2-OXOPYRROLIDIN-3-YL}ETHANESULFONAMIDE × 1 CA CALCIUM ION × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.75；18% PEG6K, 50MM MES PH 5.75, 10MM CACL2, 150MM NACL
|
Resolution 1.75 Å R-free 0.212 |
| 2VH0 Structure and property based design of factor Xa inhibitors:biaryl pyrrolidin-2-ones incorporating basic heterocyclic motifs Deposited 2007-11-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
Not recorded | CA CALCIUM ION × 1 MG MAGNESIUM ION × 1 GSI 2-(5-chlorothiophen-2-yl)-N-[(3S)-1-(4-{2-[(dimethylamino)methyl]-1H-imidazol-1-yl}-2-fluorophenyl)-2-oxopyrrolidin-3-yl]ethanesulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.85；CRYSTALLISATION WAS CARRIED OUT USING THE HANGING DROP VAPOUR DIFFUSION METHOD IN 2UL DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN AND WELL SOLUTION. WELL SOLUTION CONTAINED 16-20% PEG 6K, 50MM MES-NAOH (PH5.7-6.0), 5MM CACL2 AND 50MM NACL., pH 5.85
|
Resolution 1.70 Å R-free 0.216 |
| 2VH6 Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with biaryl P4 motifs Deposited 2007-11-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
Not recorded | GSV 2-(5-chlorothiophen-2-yl)-N-{(3S)-1-[3-fluoro-2'-(methylsulfonyl)biphenyl-4-yl]-2-oxopyrrolidin-3-yl}ethanesulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.85；CRYSTALLISATION WAS CARRIED OUT USING THE HANGING DROP VAPOUR DIFFUSION METHOD IN 2UL DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN AND WELL SOLUTION. WELL SOLUTION CONTAINED 16-20% PEG 6K, 50MM MES-NAOH (PH5.7-6.0), 5MM CACL2 AND 50MM NACL, pH 5.85
|
Resolution 1.95 Å R-free 0.242 |
| 2VVC Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-05 | Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–475（241 aa）
Fragment：PEPTIDASE S1 DOMAIN, RESIDUES 235-475
Chain L
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Mutation：YES | LZF 5-chloro-N-[(3S,4S)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-4-methoxypyrrolidin-3-yl]thiophene-2-carboxamide × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.95 Å R-free 0.275 |
| 2VVC Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-05 | Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
235–475（241 aa）
Fragment：PEPTIDASE S1 DOMAIN, RESIDUES 235-475
Chain K
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Mutation：YES | LZF 5-chloro-N-[(3S,4S)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-4-methoxypyrrolidin-3-yl]thiophene-2-carboxamide × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.95 Å R-free 0.275 |
| 2VVC Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
235–475（241 aa）
Fragment：PEPTIDASE S1 DOMAIN, RESIDUES 235-475
|
Mutation：YES | LZF 5-chloro-N-[(3S,4S)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-4-methoxypyrrolidin-3-yl]thiophene-2-carboxamide × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.95 Å R-free 0.275 |
| 2VVC Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain L
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.95 Å R-free 0.275 |
| 2VVC Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
235–475（241 aa）
Fragment：PEPTIDASE S1 DOMAIN, RESIDUES 235-475
|
Mutation：YES | LZF 5-chloro-N-[(3S,4S)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-4-methoxypyrrolidin-3-yl]thiophene-2-carboxamide × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.95 Å R-free 0.275 |
| 2VVC Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain K
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.95 Å R-free 0.275 |
| 2VVU Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-11 | Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–475（241 aa）
Fragment：CATALYTIC, RESIDUES 235-475
Chain L
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Mutation：YES | H22 5-chloro-N-[(3R)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)pyrrolidin-3-yl]thiophene-2-carboxamide × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å R-free 0.309 |
| 2VVU Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
235–475（241 aa）
Fragment：CATALYTIC, RESIDUES 235-475
|
Mutation：YES | H22 5-chloro-N-[(3R)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)pyrrolidin-3-yl]thiophene-2-carboxamide × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å R-free 0.309 |
| 2VVU Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain L
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.30 Å R-free 0.309 |
| 2VVV Aminopyrrolidine-related triazole Factor Xa inhibitor Deposited 2008-06-12 | Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–475（241 aa）
Fragment：CATALYTIC, RESIDUES 235-475
Chain L
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Mutation：YES | H21 5-chloro-N-[1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-1H-1,2,4-triazol-3-yl]thiophene-2-carboxamide × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.73 Å R-free 0.251 |
| 2VVV Aminopyrrolidine-related triazole Factor Xa inhibitor Deposited 2008-06-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
235–475（241 aa）
Fragment：CATALYTIC, RESIDUES 235-475
|
Mutation：YES | H21 5-chloro-N-[1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-1H-1,2,4-triazol-3-yl]thiophene-2-carboxamide × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.73 Å R-free 0.251 |
| 2VVV Aminopyrrolidine-related triazole Factor Xa inhibitor Deposited 2008-06-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain L
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.73 Å R-free 0.251 |
| 2VWL Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-26 | Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–475（241 aa）
Fragment：PEPTIDASE S1, RESIDUES 235-475
Chain L
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Mutation：YES | LZH 5-CHLORO-THIOPHENE-2-CARBOXYLIC ACID ((3R,5S)-1-{[2-FLUORO-4-(2-OXO-PYRIDIN-1-YL)-PHENYLCARBAMOYL]-METHYL}-5-HYDROXYMETHYL-PYRROLIDIN-3-YL)-AMIDE × 1 CL CHLORIDE ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å R-free 0.250 |
| 2VWL Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
235–475（241 aa）
Fragment：PEPTIDASE S1, RESIDUES 235-475
|
Mutation：YES | LZH 5-CHLORO-THIOPHENE-2-CARBOXYLIC ACID ((3R,5S)-1-{[2-FLUORO-4-(2-OXO-PYRIDIN-1-YL)-PHENYLCARBAMOYL]-METHYL}-5-HYDROXYMETHYL-PYRROLIDIN-3-YL)-AMIDE × 1 CL CHLORIDE ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å R-free 0.250 |
| 2VWL Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain L
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å R-free 0.250 |
| 2VWM Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-26 | Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–475（241 aa）
Fragment：PEPTIDASE S1 DOMAIN, RESIDUES 235-475
Chain L
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Mutation：YES | LZI (4R)-4-{[(5-chlorothiophen-2-yl)carbonyl]amino}-N-(cyclopropylmethyl)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-L-prolinamide × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.96 Å R-free 0.273 |
| 2VWM Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-26 | Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
235–475（241 aa）
Fragment：PEPTIDASE S1 DOMAIN, RESIDUES 235-475
Chain K
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Mutation：YES | LZI (4R)-4-{[(5-chlorothiophen-2-yl)carbonyl]amino}-N-(cyclopropylmethyl)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-L-prolinamide × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.96 Å R-free 0.273 |
| 2VWM Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
235–475（241 aa）
Fragment：PEPTIDASE S1 DOMAIN, RESIDUES 235-475
|
Mutation：YES | LZI (4R)-4-{[(5-chlorothiophen-2-yl)carbonyl]amino}-N-(cyclopropylmethyl)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-L-prolinamide × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.96 Å R-free 0.273 |
| 2VWM Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain L
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.96 Å R-free 0.273 |
| 2VWM Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
235–475（241 aa）
Fragment：PEPTIDASE S1 DOMAIN, RESIDUES 235-475
|
Mutation：YES | LZI (4R)-4-{[(5-chlorothiophen-2-yl)carbonyl]amino}-N-(cyclopropylmethyl)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-L-prolinamide × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.96 Å R-free 0.273 |
| 2VWM Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain K
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.96 Å R-free 0.273 |
| 2VWN Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-26 | Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–475（241 aa）
Fragment：PEPTIDASE S1 DOMAIN, RESIDUES 235-475
Chain L
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Mutation：YES | H25 5-Chloro-thiophene-2-carboxylic acid ((3S,4S)-1-{[2-fluoro-4-(2-oxo-2H-pyridin-1-yl)-phenylcarbamoyl]-methyl}-4-hydroxy-pyrrolidin-3-yl)-amide × 1 CA CALCIUM ION × 1 NA SODIUM ION × 2 CL CHLORIDE ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.61 Å R-free 0.228 |
| 2VWN Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
235–475（241 aa）
Fragment：PEPTIDASE S1 DOMAIN, RESIDUES 235-475
|
Mutation：YES | H25 5-Chloro-thiophene-2-carboxylic acid ((3S,4S)-1-{[2-fluoro-4-(2-oxo-2H-pyridin-1-yl)-phenylcarbamoyl]-methyl}-4-hydroxy-pyrrolidin-3-yl)-amide × 1 CA CALCIUM ION × 1 NA SODIUM ION × 2 CL CHLORIDE ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.61 Å R-free 0.228 |
| 2VWN Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain L
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.61 Å R-free 0.228 |
| 2VWO Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-26 | Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–475（241 aa）
Fragment：PEPTIDASE S1 DOMAIN, RESIDUES 235-475
Chain L
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Mutation：YES | LZG 5-CHLORO-THIOPHENE-2-CARBOXYLIC ACID ((3S,4S)-4-FLUORO- 1-{[2-FLUORO-4-(2-OXO-2H-PYRIDIN-1-YL)-PHENYLCARBAMOYL]-METHYL}-PYRROLIDIN-3-YL)-AMIDE × 1 CA CALCIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.60 Å R-free 0.228 |
| 2VWO Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
235–475（241 aa）
Fragment：PEPTIDASE S1 DOMAIN, RESIDUES 235-475
|
Mutation：YES | LZG 5-CHLORO-THIOPHENE-2-CARBOXYLIC ACID ((3S,4S)-4-FLUORO- 1-{[2-FLUORO-4-(2-OXO-2H-PYRIDIN-1-YL)-PHENYLCARBAMOYL]-METHYL}-PYRROLIDIN-3-YL)-AMIDE × 1 CA CALCIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.60 Å R-free 0.228 |
| 2VWO Aminopyrrolidine Factor Xa inhibitor Deposited 2008-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain L
126–180（55 aa）
Fragment：EGF2, RESIDUES 126-180
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.60 Å R-free 0.228 |
| 2W26 Factor Xa in complex with BAY59-7939 Deposited 2008-10-24 | Different construct Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：RESIDUES 235-468
Chain B
129–177（49 aa）
Fragment：RESIDUES 129-177
|
Not recorded | RIV 5-chloro-N-({(5S)-2-oxo-3-[4-(3-oxomorpholin-4-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)thiophene-2-carboxamide × 1 CA CALCIUM ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.08 Å R-free 0.259 |
| 2W3I Crystal Structure of FXa in complex with 4,4-disubstituted pyrrolidine-1,2-dicarboxamide inhibitor 2 Deposited 2008-11-12 | Different construct Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：HEAVY CHAIN, RESIDUES 235-468
Chain B
128–178（51 aa）
Fragment：LIGHT CHAIN, RESIDUES 128-178
|
Not recorded | CA CALCIUM ION × 1 L1C (2R,4S)-N^1^-(4-chlorophenyl)-4-(2,4-difluorophenyl)-4-hydroxy-N^2^-(2-oxo-2H-1,3'-bipyridin-6'-yl)pyrrolidine-1,2-dicarboxamide × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.90 Å R-free 0.261 |
| 2W3K Crystal Structure of FXa in complex with 4,4-disubstituted pyrrolidine-1,2-dicarboxamide inhibitor 1 Deposited 2008-11-12 | Different construct Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：HEAVY CHAIN, RESIDUES 235-468
Chain B
128–178（51 aa）
Fragment：LIGHT CHAIN, RESIDUES 128-178
|
Not recorded | L1D (2R,4S)-N^1^-(4-chlorophenyl)-N^2^-[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]-4-hydroxy-4-phenylpyrrolidine-1,2-dicarboxamide × 1 CA CALCIUM ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.05 Å R-free 0.255 |
| 2WYG Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with monoaryl P4 motifs Deposited 2009-11-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
Not recorded | 461 (E)-2-(5-CHLOROTHIOPHEN-2-YL)-N-[(3S)-1-{4-[(1R)-1-(DIMETHYLAMINO)ETHYL]-2-FLUOROPHENYL}-2-OXOPYRROLIDIN-3-YL]ETHENESULFONAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.75；CRYSTALLISATION WAS CARRIED OUT USING VAPOUR DIFFUSION IN 2UL DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN AND WELL SOLUTION. WELL SOLUTION CONTAINED 16-20% PEG6K, 50MM MES-NAOH (PH5.5-6), 5MM CACL2 AND 50MM NACL., pH 5.75
|
Resolution 1.88 Å R-free 0.234 |
| 2WYJ Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with monoaryl P4 motifs Deposited 2009-11-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 235-488
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
Not recorded | 898 (E)-2-(5-CHLOROTHIOPHEN-2-YL)-N-[(3S)-1-{4-[(1S)-1-(DIMETHYLAMINO)ETHYL]-2-FLUOROPHENYL}-2-OXOPYRROLIDIN-3-YL]ETHENESULFONAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.75；CRYSTALLISATION WAS CARRIED OUT USING HANG DROP VAPOUR DIFFUSION METHODS IN 2UL DROPS CONTAINING 1:1 RATIO PROTEIN AND WELL SOLUTION. WELL SOLUTION CONTAINED 16-20% PEG6K, 50MM MES-NAOH (PH5.5-6), 5MM CACL2 AND 50MM NACL, pH 5.75
|
Resolution 2.38 Å R-free 0.255 |
| 2XBV Factor Xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor Deposited 2010-04-15 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–475（241 aa）
Fragment：HEAVY CHAIN, RESIDUES 235-475
Chain L
126–180（55 aa）
Fragment：LIGHTCHAIN, RESIDUES 126-180
|
Mutation：YES | XBV (3R,4R)-1-(2,2-DIFLUORO-ETHYL)-PYRROLIDINE-3,4-DICARBOXYLIC ACID 3-[(5-CHLORO-PYRIDIN-2-YL)-AMIDE]-4-{[2-FLUORO-4-(2-OXO-2H-PYRIDIN-1-YL)-PHENYL]-AMIDE} × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；PH 6.5
|
Resolution 1.66 Å R-free 0.224 |
| 2XBW Factor Xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor Deposited 2010-04-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–475（241 aa）
Fragment：HEAVY CHAIN, RESIDUES 235-475
Chain L
126–180（55 aa）
Fragment：LIGHT CHAIN, RESIDUES 126-180
|
Not recorded | 455 (3R,4R)-1-SULFAMOYL-PYRROLIDINE-3,4-DICARBOXYLIC ACID 3-[(4-CHLORO-PHENYL)-AMIDE] 4-{[2-FLUORO-4-(2-OXO-2H-PYRIDIN-1-YL)-PHENYL]-AMIDE} × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；PH 6.5
|
Resolution 1.72 Å R-free 0.218 |
| 2XBX Factor Xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor Deposited 2010-04-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–475（241 aa）
Fragment：HEAVY CHAIN, RESIDUES 235-475
Chain L
126–180（55 aa）
Fragment：LIGHTCHAIN, RESIDUES 126-180
|
Not recorded | RR8 (3R,4R)-1-METHANESULFONYL-PYRROLIDINE-3,4-DICARBOXYLIC ACID 3-[(4-CHLORO-PHENYL)-AMIDE] 4-{[2-FLUORO-4-(2-OXO-2H-PYRIDIN-1-YL)-PHENYL]-AMIDE} × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；PH 6.5
|
Resolution 1.85 Å R-free 0.235 |
| 2XBY Factor Xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor Deposited 2010-04-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–475（241 aa）
Fragment：HEAVY CHAIN, RESIDUES 235-475
Chain L
126–180（55 aa）
Fragment：LIGHT CHAIN, RESIDUES 126-180
|
Not recorded | 63C (3R,4R)-1-METHYLCARBAMOYLMETHYL-PYRROLIDINE-3,4-DICARBOXYLIC ACID 3-[(4-CHLORO-PHENYL)-AMIDE] 4-{[2-FLUORO-4-(2-OXO-2H-PYRIDIN-1-YL)-PHENYL]-AMIDE} × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；PH 6.5
|
Resolution 2.02 Å R-free 0.246 |
| 2XC0 Factor Xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor Deposited 2010-04-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–475（241 aa）
Fragment：HEAVY CHAIN, RESIDUES 235-475
Chain L
126–180（55 aa）
Fragment：LIGHTCHAIN, RESIDUES 126-180
|
Not recorded | 8NC (3R,4R)-1-METHANESULFONYL-PYRROLIDINE-3,4--DICARBOXYLIC ACID 3-[(3-FLUORO-4-METHOXY-PHENYL)-AMIDE] 4-{[2-FLUORO-4-(2-OXO-2H-PYRIDIN-1-YL)-PHENYL]-AMIDE} × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；PH 6.5
|
Resolution 2.05 Å R-free 0.240 |
| 2XC4 Factor Xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor Deposited 2010-04-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–475（241 aa）
Fragment：HEAVY CHAIN, RESIDUES 235-475
Chain L
126–180（55 aa）
Fragment：LIGHT CHAIN, RESIDUES 126-180
|
Not recorded | CA CALCIUM ION × 1 NA SODIUM ION × 1 IVK (3R,4R)-N-(4-CHLOROPHENYL)-N'-[2-FLUORO-4-(2-OXOPYRIDIN-1(2H)-YL)PHENYL]-1-(2,2,2-TRIFLUOROETHYL)PYRROLIDINE-3,4-DICARBOXAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；PH 6.5
|
Resolution 1.67 Å R-free 0.244 |
| 2XC5 Factor Xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor Deposited 2010-04-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–475（241 aa）
Fragment：HEAVY CHAIN, RESIDUES 235-475
Chain L
126–180（55 aa）
Fragment：LIGHTCHAIN, RESIDUES 126-180
|
Not recorded | OYJ (3R,4R)-1-METHANESULFONYL-PYRROLIDINE-3,4-DICARBOXYLIC ACID 3-[(4-CHLORO-3-FLUORO-PHENYL)-AMIDE] 4-{[2-FLUORO-4-(2-OXO-2H-PYRIDIN-1-YL)-PHENYL]-AMIDE} × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；PH 6.5
|
Resolution 1.70 Å R-free 0.232 |
| 2Y5F FACTOR XA - CATION INHIBITOR COMPLEX Deposited 2011-01-13 | Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：RESIDUES 235-468
Chain L
127–180（54 aa）
Fragment：RESIDUES 127-180
|
Mutation：YES | XWG (3AS,4R,5S,8AS,8BR)-4-[5-(5-CHLOROTHIOPHEN-2-YL)-1,2-OXAZOL-3-YL]-2-[3-[1-(2-HYDROXYETHYL)PYRROLIDIN-1-IUM-1-YL]PROPYL]-4,6,7,8,8A,8B-HEXAHYDRO-3AH-PYRROLO[3,4-A]PYRROLIZINE-1,3-DIONE × 1 NA SODIUM ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.29 Å R-free 0.175 |
| 2Y5G FACTOR XA - CATION INHIBITOR COMPLEX Deposited 2011-01-13 | Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：RESIDUES 235-468
Chain L
127–180（54 aa）
Fragment：RESIDUES 127-180
|
Mutation：YES | FJD 3-[(3AS,4R,5S,8AS,8BR)-4-[5-(5-CHLOROTHIOPHEN-2-YL)-1,3-OXAZOL-2-YL]-1,3-DIOXO-4,6,7,8,8A,8B-HEXAHYDRO-3AH-PYRROLO[3,4-A]PYRROLIZIN-2-YL]PROPYL-TRIMETHYL-AZANIUM × 1 NA SODIUM ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.29 Å R-free 0.186 |
| 2Y5H FACTOR XA - CATION INHIBITOR COMPLEX Deposited 2011-01-13 | Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：RESIDUES 235-468
Chain L
127–180（54 aa）
Fragment：RESIDUES 127-180
|
Mutation：YES | Y5H 3-[(3AS,4R,5S,8AS,8BR)-4-[2-(5-CHLOROTHIOPHEN-2-YL)-1,3-OXAZOL-4-YL]-1,3-DIOXO-4,6,7,8,8A,8B-HEXAHYDRO-3AH-PYRROLO[3,4-A]PYRROLIZIN-2-YL]PROPYL-TRIMETHYL-AZANIUM × 1 NA SODIUM ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.33 Å R-free 0.190 |
| 2Y7X The discovery of potent and long-acting oral factor Xa inhibitors with tetrahydroisoquinoline and benzazepine P4 motifs Deposited 2011-02-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
Not recorded | MZA 6-CHLORO-N-[(3S)-1-(5-FLUORO-1,2,3,4-TETRAHYDROISOQUINOLIN-6-YL)-2-OXO-PYRROLIDIN-3-YL]NAPHTHALENE-2-SULFONAMIDE × 1 CA CALCIUM ION × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.75；16-20% PEG 6K, 50 MM MES PH 5.5-6, 5 MM CACL2, 50 MM NACL WITH SEEDING.
|
Resolution 1.90 Å R-free 0.230 |
| 2Y7Z Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with aminoindane and phenylpyrrolidine P4 motifs Deposited 2011-02-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
Not recorded | C0Z 6-CHLORO-N-[(3S)-1-[(1S)-1-DIMETHYLAMINO-2,3-DIHYDRO-1H-INDEN-5-YL]-2-OXO-PYRROLIDIN-3-YL]NAPHTHALENE-2-SULFONAMIDE × 1 CA CALCIUM ION × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.75；CRYSTALLISATION WAS CARRIED OUT USING VAPOUR DIFFUSION IN 2UL DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN AND WELL SOLUTION. WELL SOLUTION CONTAINED 16-20% PEG6K, 50MM MES-NAOH (PH 5.5-6), 5MM CACL2 AND 50MM NACL.
|
Resolution 1.84 Å R-free 0.246 |
| 2Y80 Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with aminoindane and phenylpyrrolidine P4 motifs Deposited 2011-02-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
Not recorded | 439 6-CHLORO-N-{(3S)-1-[(1S)-1-(DIMETHYLAMINO)-2,3-DIHYDRO-1H-INDEN-5-YL]-2-OXO-3-PYRROLIDINYL}-2-NAPHTHALENESULFONAMIDE × 1 CA CALCIUM ION × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.75；CRYSTALLISATION WAS CARRIED OUT USING VAPOUR DIFFUSION IN 2UL DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN AND WELL SOLUTION. WELL SOLUTION CONTAINED 16-20% PEG 6K, 50 MM MES-NAOH (PH 5.5-6), 5 MM CACL2 AND 50 MM NACL.
|
Resolution 1.90 Å R-free 0.241 |
| 2Y81 Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with aminoindane and phenylpyrrolidine P4 motifs Deposited 2011-02-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
Not recorded | 931 6-CHLORO-N-((3S)-2-OXO-1-{4-[(2R)-2--PYRROLIDINYL] PHENYL}-3-PYRROLIDINYL)-2-NAPHTHALENESULFONAMIDE × 1 CA CALCIUM ION × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.75；CRYSTALLISATION WAS CARRIED OUT USING VAPOUR DIFFUSION IN 2UL DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN AND WELL SOLUTION. WELL SOLUTION CONTAINED 16-20% PEG 6K, 50 MM MES-NAOH (PH 5.5-6), 5 MM CACL2 AND 50 MM NACL.
|
Resolution 1.70 Å R-free 0.225 |
| 2Y82 Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with aminoindane and phenylpyrrolidine P4 motifs Deposited 2011-02-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Chain B
46–179（134 aa）
Fragment：ACTIVATED DESGLA, RESIDUES 46-179
|
Not recorded | 930 6-CHLORO-N-((3S)-2-OXO-1-{4-[(2S)-2-PYRROLIDINYL]PHENYL}-3-PYRROLIDINYL)-2-NAPHTHALENESULFONAMIDE × 1 CA CALCIUM ION × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.75；CRYSTALLISATION WAS CARRIED OUT USING VAPOUR DIFFUSION IN 2UL DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN AND WELL SOLUTION. WELL SOLUTION CONTAINED 16-20% PEG 6K, 50 MM MES-NAOH (PH 5.5-6), 5 MM CACL2 AND 50 MM NACL.
|
Resolution 2.20 Å R-free 0.233 |
| 3CEN Factor XA in complex with the inhibitor N-(2-(((5-chloro-2-pyridinyl) amino)sulfonyl)phenyl)-4-(2-oxo-1(2H)-pyridinyl)benzamide Deposited 2008-02-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：Activated factor Xa heavy chain, UNP residues 235-468
Chain L
127–178（52 aa）
Fragment：UNP residues 127-178
|
Not recorded | FXA N-(2-(((5-CHLORO-2-PYRIDINYL)AMINO)SULFONYL)PHENYL)-4-(2-OXO-1(2H)-PYRIDINYL)BENZAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；200 mM Sodium Acetate, pH 5.5, 18% PEG6000, vapor diffusion, hanging drop, temperature 277K
|
Resolution 1.60 Å R-free 0.294 |
| 3CS7 FACTOR XA IN COMPLEX WITH THE INHIBITOR 1-(4-methoxyphenyl)-6-(4-(1-(pyrrolidin-1-ylmethyl)cyclopropyl)phenyl)-3-(trifluoromethyl)-5,6-dihydro-1H-pyrazolo[3,4-c]pyridin-7(4H)-one Deposited 2008-04-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：Coagulation Factor X, Heavy Chain
Chain L
127–178（52 aa）
Fragment：Coagulation Factor X, Light Chain
|
Not recorded | CA CALCIUM ION × 1 LG0 1-(4-methoxyphenyl)-6-(4-(1-(pyrrolidin-1-ylmethyl)cyclopropyl)phenyl)-3-(trifluoromethyl)-5,6-dihydro-1H-pyrazolo[3,4-c]pyridin-7(4H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；277 K；200 mM Sodium Acetate, pH 5.5, 18% PEG6000, vapor diffusion, hanging drop, temperature 277K, pH 5.50
|
Resolution 2.20 Å R-free 0.274 |
| 3ENS Crystal structure of human FXA in complex with methyl (2Z)-3-[(3-chloro-1H-indol-7-yl)amino]-2-cyano-3-{[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]amino}acrylate Deposited 2008-09-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
85–178（94 aa）
Fragment：sequence database residues 93-178
Chain B
235–472（238 aa）
Fragment：sequence database residues 235-472
|
Not recorded | GOL GLYCEROL × 4 ENS methyl (2Z)-3-[(3-chloro-1H-indol-7-yl)amino]-2-cyano-3-{[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]amino}acrylate × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；298 K；15-22% W/V PEG MME 5000, 0.01 M CALCIUM ACETATE, 0.35 M SODIUM ACETATE, 0.1 M LITHIUM SULFATE, 0.1 M MES, pH 6.500000, VAPOR DIFFUSION HANGING DROP, temperature 298K, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.30 Å R-free 0.286 |
| 3ENS Crystal structure of human FXA in complex with methyl (2Z)-3-[(3-chloro-1H-indol-7-yl)amino]-2-cyano-3-{[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]amino}acrylate Deposited 2008-09-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
85–178（94 aa）
Fragment：sequence database residues 93-178
Chain D
235–472（238 aa）
Fragment：sequence database residues 235-472
|
Not recorded | GOL GLYCEROL × 3 ENS methyl (2Z)-3-[(3-chloro-1H-indol-7-yl)amino]-2-cyano-3-{[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]amino}acrylate × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；298 K；15-22% W/V PEG MME 5000, 0.01 M CALCIUM ACETATE, 0.35 M SODIUM ACETATE, 0.1 M LITHIUM SULFATE, 0.1 M MES, pH 6.500000, VAPOR DIFFUSION HANGING DROP, temperature 298K, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.30 Å R-free 0.286 |
| 3FFG Factor XA in complex with the inhibitor (R)-6-(2'-((3- HYDROXYPYRROLIDIN-1-YL)METHYL)BIPHENYL-4-YL)-1-(3-(5-OXO-4,5-DIHYDRO-1H-1,2,4-TRIAZOL-3-YL)PHENYL)-3-(TRIFLUOROMETHYL)-5,6-DIHYDRO-1H-PYRAZOLO[3,4-C]PYRIDIN- 7(4H)-ONE Deposited 2008-12-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：sequence database residues 235-468
Chain L
127–178（52 aa）
Fragment：sequence database residues 127-178
|
Not recorded | FFG (R)-6-(2'-((3-hydroxypyrrolidin-1-yl)methyl)biphenyl-4-yl)-1-(3-(5-oxo-4,5-dihydro-1h-1,2,4-triazol-3-yl)phenyl)-3-(trifluoromethyl)-5,6-dihydro-1h-pyrazolo[3,4-c]pyridin-7(4h)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；200 mM Sodium Acetate, pH 5.5, 18% PEG6000, vapor diffusion, hanging drop, temperature 277K
|
Resolution 1.54 Å R-free 0.240 |
| 3HPT Crystal structure of human FxA in complex with (S)-2-cyano-1-(2-methylbenzofuran-5-yl)-3-(2-oxo-1-(2-oxo-2-(pyrrolidin-1-yl)ethyl)azepan-3-yl)guanidine Deposited 2009-06-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
85–178（94 aa）
Fragment：Factor X light chain: UNP residues 85-178
Chain B
235–472（238 aa）
Fragment：Activated factor Xa heavy chain: UNP residues 235-472
|
Not recorded | GOL GLYCEROL × 3 YET 1-cyano-2-(2-methyl-1-benzofuran-5-yl)-3-[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]guanidine × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ACT ACETATE ION × 4 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；15-22% w/v PEG MME 5000, 0.01 M Calcium acetate, 0.35 M Sodium acetate, 0.1 M Lithium sulfate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.19 Å R-free 0.239 |
| 3HPT Crystal structure of human FxA in complex with (S)-2-cyano-1-(2-methylbenzofuran-5-yl)-3-(2-oxo-1-(2-oxo-2-(pyrrolidin-1-yl)ethyl)azepan-3-yl)guanidine Deposited 2009-06-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
85–178（94 aa）
Fragment：Factor X light chain: UNP residues 85-178
Chain D
235–472（238 aa）
Fragment：Activated factor Xa heavy chain: UNP residues 235-472
|
Not recorded | GOL GLYCEROL × 2 YET 1-cyano-2-(2-methyl-1-benzofuran-5-yl)-3-[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]guanidine × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ACT ACETATE ION × 4 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；15-22% w/v PEG MME 5000, 0.01 M Calcium acetate, 0.35 M Sodium acetate, 0.1 M Lithium sulfate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.19 Å R-free 0.239 |
| 3IIT Factor XA in complex with a cis-1,2-diaminocyclohexane derivative Deposited 2009-08-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–467（233 aa）
Chain B
125–178（54 aa）
Fragment：UNP RESIDUES 125-178
|
Not recorded | CA CALCIUM ION × 2 D14 7-chloro-N-[(1S,2R,4S)-4-(dimethylcarbamoyl)-2-{[(5-methyl-5,6-dihydro-4H-pyrrolo[3,4-d][1,3]thiazol-2-yl)carbonyl]amino}cyclohexyl]isoquinoline-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5；293 K；pH 5.00, VAPOR DIFFUSION, temperature 293K
|
Resolution 1.80 Å R-free 0.233 |
| 3K9X X-ray crystal structure of human fxa in complex with (S)-N-((2-METHYLBENZOFURAN-5-YLAMINO)(2-OXO-1-(2-OXO-2- (PYRROLIDIN-1-YL)ETHYL)AZEPAN-3- YLAMINO)METHYLENE)NICOTINAMIDE Deposited 2009-10-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
85–178（94 aa）
Fragment：EGF-LIKE DOMAINS (UNP residues 85 to 178)
Chain B
235–472（238 aa）
Fragment：CATALYTIC DOMAINS (UNP residues 235 to 472)
|
Not recorded | GOL GLYCEROL × 5 MBM N-{N'-(2-methyl-1-benzofuran-5-yl)-N-[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]carbamimidoyl}pyridine-3-carboxamide × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；15-22% W/V PEG MME 5000, 0.01 M CALCIUM ACETATE, 0.35 M SODIUM ACETATE, 0.1 M LITHIUM SULFATE, 0.1 M MES, pH 6.0, VAPOR DIFFUSION HANGING DROP, temperature 298K
|
Resolution 1.90 Å R-free 0.240 |
| 3K9X X-ray crystal structure of human fxa in complex with (S)-N-((2-METHYLBENZOFURAN-5-YLAMINO)(2-OXO-1-(2-OXO-2- (PYRROLIDIN-1-YL)ETHYL)AZEPAN-3- YLAMINO)METHYLENE)NICOTINAMIDE Deposited 2009-10-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
85–178（94 aa）
Fragment：EGF-LIKE DOMAINS (UNP residues 85 to 178)
Chain D
235–472（238 aa）
Fragment：CATALYTIC DOMAINS (UNP residues 235 to 472)
|
Not recorded | GOL GLYCEROL × 1 MBM N-{N'-(2-methyl-1-benzofuran-5-yl)-N-[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]carbamimidoyl}pyridine-3-carboxamide × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；15-22% W/V PEG MME 5000, 0.01 M CALCIUM ACETATE, 0.35 M SODIUM ACETATE, 0.1 M LITHIUM SULFATE, 0.1 M MES, pH 6.0, VAPOR DIFFUSION HANGING DROP, temperature 298K
|
Resolution 1.90 Å R-free 0.240 |
| 3KL6 Discovery of Tetrahydropyrimidin-2(1H)-one derivative TAK-442: A potent, selective and orally active factor Xa inhibitor Deposited 2009-11-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–475（241 aa）
Fragment：Factor X heavy chain residues 235-475
Chain B
126–179（54 aa）
Fragment：Factor X light chain residues 126-179
|
Not recorded | 443 1-(1-{(2S)-3-[(6-chloronaphthalen-2-yl)sulfonyl]-2-hydroxypropanoyl}piperidin-4-yl)tetrahydropyrimidin-2(1H)-one × 1 EDO 1,2-ETHANEDIOL × 4 CA CALCIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；25.% .PEG 3350, 0.1M .tris pH 8.5 , VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.45 Å R-free 0.212 |
| 3KQB Factor xa in complex with the inhibitor n-(3-fluoro-2'- (methylsulfonyl)biphenyl-4-yl)-1-(3-(5-oxo-4,5-dihydro-1h- 1,2,4-triazol-3-yl)phenyl)-3-(trifluoromethyl)-1h- pyrazole-5-carboxamide Deposited 2009-11-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：residues 235-468 of factor X uncleaved sequence
Chain L
127–178（52 aa）
Fragment：residues 127-178 of factor X uncleaved sequence
|
Not recorded | LGJ N-(3-FLUORO-2'-(METHYLSULFONYL)BIPHENYL-4-YL)-1-(3-(5-OXO-4,5-DIHYDRO-1H-1,2,4-TRIAZOL-3-YL)PHENYL)-3-(TRIFLUOROMETHYL)-1H-PYRAZOLE-5-CARBOXAMIDE × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；200 mM NaOAc (pH 5.5), 18% PEG 6000, pH 5.500000, vapor diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.25 Å R-free 0.221 |
| 3KQC Factor xa in complex with the inhibitor 6-(2'- (methylsulfonyl)biphenyl-4-yl)-1-(3-(5-oxo-4,5-dihydro-1h- 1,2,4-triazol-3-yl)phenyl)-3-(trifluoromethyl)-5,6- dihydro-1h-pyrazolo[3,4-c]pyridin-7(4h)-one Deposited 2009-11-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：residues 235-468 of factor X uncleaved sequence
Chain L
127–178（52 aa）
Fragment：residues 127-178 of factor X uncleaved sequence
|
Not recorded | LGK 6-(2'-(METHYLSULFONYL)BIPHENYL-4-YL)-1-(3-(5-OXO-4,5-DIHYDRO-1H-1,2,4-TRIAZOL-3-YL)PHENYL)-3-(TRIFLUOROMETHYL)-5,6-DIHYDRO-1H-PYRAZOLO[3,4-C]PYRIDIN-7(4H)-ONE × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；200 mM NaOAc (pH 5.5), 18% PEG 6000, pH 5.500000, vapor diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.20 Å R-free 0.224 |
| 3KQD Factor xa in complex with the inhibitor 1-(3-(5-oxo-4,5- dihydro-1h-1,2,4-triazol-3-yl)phenyl)-6-(2'-(pyrrolidin-1- ylmethyl)biphenyl-4-yl)-3-(trifluoromethyl)-5,6-dihydro- 1h-pyrazolo[3,4-c]pyridin-7(4h)-one Deposited 2009-11-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：residues 235-468 of factor X uncleaved sequence
Chain L
127–178（52 aa）
Fragment：residues 127-178 of factor X uncleaved sequence
|
Not recorded | LGL 1-(3-(5-OXO-4,5-DIHYDRO-1H-1,2,4-TRIAZOL-3-YL)PHENYL)-6-(2'-(PYRROLIDIN-1-YLMETHYL)BIPHENYL-4-YL)-3-(TRIFLUOROMETHYL)-5,6-DIHYDRO-1H-PYRAZOLO[3,4-C]PYRIDIN-7(4H)-ONE × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；200 mM NaOAc (pH 5.5), 18% PEG 6000, pH 5.500000, vapor diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.75 Å R-free 0.254 |
| 3KQE Factor xa in complex with the inhibitor 3-methyl-1-(3-(5- oxo-4,5-dihydro-1h-1,2,4-triazol-3-yl)phenyl)-6-(2'- (pyrrolidin-1-ylmethyl)biphenyl-4-yl)-5,6-dihydro-1h- pyrazolo[3,4-c]pyridin-7(4h)-one Deposited 2009-11-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：residues 235-468 of factor X uncleaved sequence
Chain L
127–178（52 aa）
Fragment：residues 127-178 of factor X uncleaved sequence
|
Not recorded | LGM 3-METHYL-1-(3-(5-OXO-4,5-DIHYDRO-1H-1,2,4-TRIAZOL-3-YL)PHENYL)-6-(2'-(PYRROLIDIN-1-YLMETHYL)BIPHENYL-4-YL)-5,6-DIHYDRO-1H-PYRAZOLO[3,4-C]PYRIDIN-7(4H)-ONE × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；200 mM NaOAc (pH 5.5), 18% PEG 6000, pH 5.500000, vapor diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.35 Å R-free 0.230 |
| 3LIW Factor XA in complex with (R)-2-(1-ADAMANTYLCARBAMOYLAMINO)-3-(3-CARBAMIDOYL-PHENYL)-N-PHENETHYL-PROPIONIC ACID AMIDE Deposited 2010-01-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：UNP RESIDUES 235-468
Chain B
128–178（51 aa）
Fragment：UNP RESIDUES 128-178
|
Not recorded | CA CALCIUM ION × 2 RUP (R)-2-(3-ADAMANTAN-1-YL-UREIDO)-3-(3-CARBAMIMIDOYL-PHENYL)-N-PHENETHYL-PROPIONAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；CACL2, PEG 6000, MES, PH 5.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K
|
Resolution 2.22 Å R-free 0.266 |
| 3M36 Factor XA in complex with the inhibitor 1-[3-(aminomethyl)phenyl]-N-[3-fluoro-2'-(methylsulfonyl)biphenyl-4-yl]-3-(trifluoromethyl)-1H-pyrazole-5-carboxamide (DPC423) Deposited 2010-03-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：Peptidase S1
Chain L
127–178（52 aa）
Fragment：UNP residues 127-178
|
Not recorded | M35 1-[3-(aminomethyl)phenyl]-N-[3-fluoro-2'-(methylsulfonyl)biphenyl-4-yl]-3-(trifluoromethyl)-1H-pyrazole-5-carboxamide × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；200 mM Sodium Acetate, pH 5.5, 18% PEG6000, vapor diffusion, hanging drop, temperature 277K
|
Resolution 2.15 Å R-free 0.264 |
| 3M37 Factor XA in complex with the inhibitor 1-[2-(aminomethyl)phenyl]-N-(3-fluoro-2'-sulfamoylbiphenyl-4-yl)-3-(trifluoromethyl)-1H-pyrazole-5-carboxamide (DPC602) Deposited 2010-03-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Fragment：Peptidase S1
Chain L
127–178（52 aa）
Fragment：UNP residues 127-178
|
Not recorded | M37 1-[2-(aminomethyl)phenyl]-N-(3-fluoro-2'-sulfamoylbiphenyl-4-yl)-3-(trifluoromethyl)-1H-pyrazole-5-carboxamide × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；200 mM Sodium Acetate, pH 5.5, 18% PEG6000, vapor diffusion, hanging drop, temperature 277K
|
Resolution 1.90 Å R-free 0.262 |
| 3Q3K Factor Xa in complex with a phenylenediamine derivative Deposited 2010-12-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–467（233 aa）
Fragment：UNP RESIDUES 235-467
Chain B
125–178（54 aa）
Fragment：UNP RESIDUES 125-178
|
Not recorded | CA CALCIUM ION × 2 D90 N-(2-{[(5-chloro-1H-indol-2-yl)carbonyl]amino}phenyl)-5-methyl-4,5,6,7-tetrahydro[1,3]thiazolo[5,4-c]pyridine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；macro-seeding, soak at pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.216 |
| 3SW2 X-ray crystal structure of human FXA in complex with 6-chloro-N-((3S)-2-oxo-1-(2-oxo-2-((5S)-8-oxo-5,6-dihydro-1H-1,5-methanopyrido[1,2-a][1,5]diazocin-3(2H,4H,8H)-yl)ethyl)piperidin-3-yl)naphthalene-2-sulfonamide Deposited 2011-07-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
85–178（94 aa）
Fragment：Factor X light chain (UNP residues 85-178)
Chain B
235–472（238 aa）
Fragment：Activated factor Xa heavy chain (UNP residues 235-472)
|
Not recorded | FI1 6-chloro-N-((3S)-2-oxo-1-(2-oxo-2-((5S)-8-oxo-5,6-dihydro-1H-1,5-methanopyrido[1,2-a][1,5]diazocin-3(2H,4H,8H)-yl)ethyl)piperidin-3-yl)naphthalene-2-sulfonamide × 1 NA SODIUM ION × 1 CA CALCIUM ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；15-22% w/v PEG5000 MME, 0.01 M calcium acetate, 0.35 M sodium acetate, 0.1 M lithium sulfate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.42 Å R-free 0.262 |
| 3TK5 Factor Xa in complex with D102-4380 Deposited 2011-08-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–467（233 aa）
Fragment：UNP RESIDUES 235-467
Chain B
125–178（54 aa）
Fragment：UNP RESIDUES 125-178
|
Not recorded | CA CALCIUM ION × 2 D1Q 4-{3-[(4-chlorophenyl)amino]-3-oxopropyl}-3-({[5-(propan-2-yl)-4,5,6,7-tetrahydro[1,3]thiazolo[5,4-c]pyridin-2-yl]carbonyl}amino)benzoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.20 Å R-free 0.253 |
| 3TK6 factor Xa in complex with D46-5241 Deposited 2011-08-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–467（233 aa）
Fragment：UNP RESIDUES 235-467
Chain B
125–178（54 aa）
Fragment：UNP RESIDUES 125-178
|
Not recorded | CA CALCIUM ION × 2 D46 N-[2-({[(5-chlorothiophen-2-yl)carbonyl]amino}methyl)phenyl]-5-methyl-4,5,6,7-tetrahydro[1,3]thiazolo[5,4-c]pyridine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.80 Å R-free 0.241 |
| 4A7I Factor Xa in complex with a potent 2-amino-ethane sulfonamide inhibitor Deposited 2011-11-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
84–179（96 aa）
Fragment：DES-GLA FACTOR X LIGHT CHAIN, RESIDUES 84-179
Chain B
235–488（254 aa）
Fragment：ACTIVATED FACTOR X HEAVY CHAIN, RESIDUES 235-488
|
Not recorded | CA CALCIUM ION × 1 A7I 5-CHLORO-THIOPHENE-2-CARBOXYLIC ACID [2-(1--ISOPROPYL-PIPERIDIN-4-YLSULFAMOYL)-ETHYL]-AMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.7；PROTEIN SOLUTION: 8 MG/ML PROTEIN, 5 MM MES (PH 5.7), 5 MM CACL2, 100 MM BENZAMIDINE. RESERVOIR: 18-20% PEG-600, 50 MM MES (PH 5.7). SOAKING: ADD 10 MM INHIBITOR.
|
Resolution 2.40 Å R-free 0.253 |
| 4BTI factor Xa in complex with the dual thrombin-FXa inhibitor 58. Deposited 2013-06-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain E
84–179（96 aa）
Chain F
235–488（254 aa）
|
Not recorded | CA CALCIUM ION × 1 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 5.7；PROTEIN SOLUTION: 8 MG/ML DESGLA FACTOR XA, 5 MM MES (PH 6.0), 5 MM CACL2, 100 MM BENZAMIDINE. RESERVOIR SOLUTION: 18-20% PEG600, 50 MM MES (PH 5.7). HANGING DROP SETUP.
|
Resolution 2.30 Å R-free 0.224 |
| 4BTI factor Xa in complex with the dual thrombin-FXa inhibitor 58. Deposited 2013-06-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
84–179（96 aa）
Chain B
235–488（254 aa）
|
Not recorded | CA CALCIUM ION × 1 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 5.7；PROTEIN SOLUTION: 8 MG/ML DESGLA FACTOR XA, 5 MM MES (PH 6.0), 5 MM CACL2, 100 MM BENZAMIDINE. RESERVOIR SOLUTION: 18-20% PEG600, 50 MM MES (PH 5.7). HANGING DROP SETUP.
|
Resolution 2.30 Å R-free 0.224 |
| 4BTT factor Xa in complex with the dual thrombin-FXa inhibitor 31. Deposited 2013-06-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain E
84–179（96 aa）
Fragment：LIGHT CHAIN, RESIDUES 84-179
Chain F
235–488（254 aa）
Fragment：HEAVY CHAIN, RESIDUES 235-488
|
Not recorded | CA CALCIUM ION × 1 VYR N-[(S)-1-[5-(5-Chloro-thiophen-2-yl)-isoxazol-3-ylmethyl]-2-(4-methoxy-piperidin-1-yl)-2-oxo-ethyl]-2-ethyl-3-(3-oxo-morpholin-4-yl)-benzenesulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；PROTEIN SOLUTION: 8 MG/ML DESGLA FACTOR XA, 5 MM MES (PH 6.0), 5 MM CACL2, 100 MM BENZAMIDINE. RESERVOIR SOLUTION: 18-20% PEG600, 50 MM MES (PH 5.7). HANGING DROP SETUP.
|
Resolution 2.59 Å R-free 0.236 |
| 4BTT factor Xa in complex with the dual thrombin-FXa inhibitor 31. Deposited 2013-06-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
84–179（96 aa）
Fragment：LIGHT CHAIN, RESIDUES 84-179
Chain B
235–488（254 aa）
Fragment：HEAVY CHAIN, RESIDUES 235-488
|
Not recorded | CA CALCIUM ION × 1 VYR N-[(S)-1-[5-(5-Chloro-thiophen-2-yl)-isoxazol-3-ylmethyl]-2-(4-methoxy-piperidin-1-yl)-2-oxo-ethyl]-2-ethyl-3-(3-oxo-morpholin-4-yl)-benzenesulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；PROTEIN SOLUTION: 8 MG/ML DESGLA FACTOR XA, 5 MM MES (PH 6.0), 5 MM CACL2, 100 MM BENZAMIDINE. RESERVOIR SOLUTION: 18-20% PEG600, 50 MM MES (PH 5.7). HANGING DROP SETUP.
|
Resolution 2.59 Å R-free 0.236 |
| 4BTU Factor Xa in complex with the dual thrombin-FXa inhibitor 57. Deposited 2013-06-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
84–179（96 aa）
Fragment：LIGHT CHAIN, RESIDUES 84-179
Chain B
235–488（254 aa）
Fragment：HEAVY CHAIN, RESIDUES 235-488
|
Not recorded | CA CALCIUM ION × 1 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 5.7；PROTEIN SOLUTION: 8 MG/ML REMARK 280 DESGLA FACTOR XA, 5 MM MES (PH 6.0), 5 MM CACL2, 100 MM REMARK 280 BENZAMIDINE. RESERVOIR SOLUTION: 18-20% PEG600, 50 MM MES REMARK 280 (PH 5.7). HANGING DROP SETUP.
|
Resolution 2.37 Å R-free 0.248 |
| 4BTU Factor Xa in complex with the dual thrombin-FXa inhibitor 57. Deposited 2013-06-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain E
84–179（96 aa）
Fragment：LIGHT CHAIN, RESIDUES 84-179
Chain F
235–488（254 aa）
Fragment：HEAVY CHAIN, RESIDUES 235-488
|
Not recorded | CA CALCIUM ION × 1 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 5.7；PROTEIN SOLUTION: 8 MG/ML REMARK 280 DESGLA FACTOR XA, 5 MM MES (PH 6.0), 5 MM CACL2, 100 MM REMARK 280 BENZAMIDINE. RESERVOIR SOLUTION: 18-20% PEG600, 50 MM MES REMARK 280 (PH 5.7). HANGING DROP SETUP.
|
Resolution 2.37 Å R-free 0.248 |
| 4Y6D Factor Xa complex with GTC000101 Deposited 2015-02-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Chain B
46–179（134 aa）
Fragment：FACTOR X LIGHT CHAIN, UNP residues 46-179
|
Not recorded | 48U 4-[(3S)-3-({[(E)-2-(5-chlorothiophen-2-yl)ethenyl]sulfonyl}amino)-2-oxopyrrolidin-1-yl]-3-fluoro-N,N-dimethylbenzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；16-20% PEG 6K, 50mM Mes-NaOH pH 5.7-6.0, 5 mM CaCl2, and 50 mM NaCl
|
Resolution 1.55 Å R-free 0.233 |
| 4Y71 Factor Xa complex with GTC000398 Deposited 2015-02-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Chain B
46–179（134 aa）
Fragment：UNP residues 46-179
|
Not recorded | CA CALCIUM ION × 1 48W 6-chloro-N-{(3S)-1-[(2S)-1-(4-methyl-5-oxo-1,4-diazepan-1-yl)-1-oxopropan-2-yl]-2-oxopyrrolidin-3-yl}naphthalene-2-sulf onamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；16 - 20 % PEG 6000, 50 mM MES-NaOH (pH 5.7-6.0), 5 mM calcium chloride, 50 mM sodium chloride
|
Resolution 1.80 Å R-free 0.240 |
| 4Y76 Factor Xa complex with GTC000401 Deposited 2015-02-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Chain B
46–179（134 aa）
Fragment：UNP residues 46-179
|
Not recorded | CA CALCIUM ION × 1 4O1 N~2~-[(6-chloronaphthalen-2-yl)sulfonyl]-N~2~-{(3S)-1-[(2S)-1-(4-methyl-1,4-diazepan-1-yl)-1-oxopropan-2-yl]-2-oxopyrrolidin-3-yl}glycinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.75；293 K；18% PEG 6000, 100 mm MES PH 5.75, 10 mm calcium chloride
|
Resolution 2.00 Å R-free 0.236 |
| 4Y79 Factor Xa complex with GTC000406 Deposited 2015-02-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Chain B
46–179（134 aa）
Fragment：UNP residues 46-179
|
Not recorded | CA CALCIUM ION × 1 MG MAGNESIUM ION × 1 4O6 (E)-2-(4-chlorophenyl)-N-{(3S)-1-[(2S)-1-(morpholin-4-yl)-1-oxopropan-2-yl]-2-oxopyrrolidin-3-yl}ethenesulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.75；293 K；18% PEG 6000, 100 mM MES PH5.75, 10 mM calcium chloride
|
Resolution 2.10 Å R-free 0.216 |
| 4Y7A Factor Xa complex with GTC000422 Deposited 2015-02-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Chain B
46–179（134 aa）
Fragment：UNP residues 46-179
|
Not recorded | CA CALCIUM ION × 1 MG MAGNESIUM ION × 1 987 N-[(3S)-1-{(2S)-1-[(3S)-3-aminopiperidin-1-yl]-1-oxopropan-2-yl}-2-oxopyrrolidin-3-yl]-6-chloronaphthalene-2-sulfonamid e × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；18% PEG 6000, 100 mM MES PH 5.75, 10 mM calcium chloride
|
Resolution 1.99 Å R-free 0.236 |
| 4Y7B Factor Xa complex with GTC000441 Deposited 2015-02-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Chain B
46–179（134 aa）
Fragment：UNP residues 46-179
|
Not recorded | CA CALCIUM ION × 1 44I 6-chloro-N-{(3S)-1-[(2S)-1-{(1R,5S)-7-[2-(methylamino)ethyl]-3,7-diazabicyclo[3.3.1]non-3-yl}-1-oxopropan-2-yl]-2-oxopy rrolidin-3-yl}naphthalene-2-sulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.75；293 K；18% PEG 6000, 100 mM MES PH 5.75, 10 mM calcium chloride
|
Resolution 1.79 Å R-free 0.212 |
| 4ZH8 Factor Xa complex with GTC000006 Deposited 2015-04-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Fragment：residues 235 - 488
Chain B
46–179（134 aa）
Fragment：residues 43-179
|
Not recorded | CA CALCIUM ION × 1 4O4 6-chloro-N-{(3S)-1-[(2S)-1-(morpholin-4-yl)-1-oxopropan-2-yl]-2-oxo-2,3-dihydro-1H-pyrrol-3-yl}-N-(2-oxobutyl)naphthalene-2-sulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；16-20% PEG 6K, 50 mM Mes=NaOH pH 5.7-6.0, 5 mM CaCl2 and 50 mM NaCl
|
Resolution 1.80 Å R-free 0.255 |
| 4ZHA Factor Xa complex with GTC000102 Deposited 2015-04-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–488（254 aa）
Fragment：residues 235-488
Chain B
46–179（134 aa）
Fragment：residues 46-179
|
Not recorded | CA CALCIUM ION × 1 MG MAGNESIUM ION × 1 4O5 4-[(3S)-3-({[(E)-2-(5-chlorothiophen-2-yl)ethenyl]sulfonyl}amino)-2-oxo-2,3-dihydro-1H-pyrrol-1-yl]-3-fluoro-N-methylbenzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；16-20% PEG 6K, 50 mM Mes-NaOH (pH 5.7-6.0), 5 mM CaCl2, and 50 mM NaCl
|
Resolution 1.86 Å R-free 0.238 |
| 5JQY Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, N-oxalylglycine and factor X substrate peptide fragment(39mer-4Ser) Deposited 2016-05-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
Fragment：UNP residues 86-124
|
Not recorded | MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；100mM SPG buffer, 25% PEG 1500, 2mM NOG, 1mM MnCl2, 18mg/ml protein
|
Resolution 1.99 Å R-free 0.205 |
| 5JTC Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, 2,4-pyridine dicarboxylate and factor X substrate peptide fragment(39mer-4Ser) Deposited 2016-05-09 | 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 B
86–124（39 aa）
Fragment：UNP Residues 86-124
|
Not recorded | MN MANGANESE (II) ION × 1 PD2 PYRIDINE-2,4-DICARBOXYLIC ACID × 1 BR BROMIDE ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；20% PEG3350, 200mM NaBr, 100mM BisTris Propane, 1mM MnCl2, 2mM 2,4-PDCA, 330uM ASPH, 726uM Factor X
|
Resolution 2.24 Å R-free 0.208 |
| 5JZ8 Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, N-oxalylglycine, and factor X substrate peptide fragment (39mer) Deposited 2016-05-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM Bis-tris propane, 200mM sodium acetate, 20% PEG 3350, 1 mM manganese chloride, 2 mM N-oxalylglycine, 726 uM FX peptide, 18 mg/ml protein
|
Resolution 2.10 Å R-free 0.216 |
| 5JZU Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, N-oxalylglycine and factor X substrate peptide fragment (26mer) Deposited 2016-05-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–111（26 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM Bis-tris propane, 20 mM sodium/potassium phosphate, 20% PEG 3350, 1 mM manganese chloride, 2 mM N-oxalylglycine, 1.65 mM factor X peptide, 18 mg/ml asph protein
|
Resolution 2.50 Å R-free 0.229 |
| 5K0H Human factor Xa in complex with synthetic inhibitor benzylsulfonyl-dSer(Benzyl)-Gly-4-amidinobenzylamide Deposited 2016-05-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Chain B
128–178（51 aa）
|
Not recorded | CA CALCIUM ION × 2 6PK O-benzyl-N-(benzylsulfonyl)-D-seryl-N-[(4-carbamimidoylphenyl)methyl]glycinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, 12-18 % PEG6000, 5 mM CaCl2
|
Resolution 2.20 Å R-free 0.261 |
| 5VOE DesGla-XaS195A Bound to Aptamer 11F7t Deposited 2017-05-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
235–467（233 aa）
Fragment：residues 235-467
Chain L
128–178（51 aa）
Fragment：residues 128-178
|
Mutation：S419A | NA SODIUM ION × 1 CA CALCIUM ION × 1 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.1 M Bicine, 0.1 M Tris base, 0.1 M Carboxylic Acids, 10% PEG 20,000, 20% PEG 500 monomethyl ester
|
Resolution 2.00 Å R-free 0.248 |
| 5VOF DesGla-XaS195A Bound to Aptamer 11F7t and Rivaroxaban Deposited 2017-05-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric |
Chain H
235–467（233 aa）
Fragment：residue 235-467
Chain L
128–178（51 aa）
Fragment：residues 128-178
|
Mutation：S419A | RIV 5-chloro-N-({(5S)-2-oxo-3-[4-(3-oxomorpholin-4-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)thiophene-2-carboxamide × 1 NA SODIUM ION × 1 CA CALCIUM ION × 1 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.1 M Bicine, 0.1 M Tris base, 0.1 M Carboxylic acids, 10% PEG 20,000, 20% PEG 500 MME
|
Resolution 2.25 Å R-free 0.253 |
| 6Q9F Aspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in complex with Mn, NOG and Factor X peptide fragment (39mer-4Ser) Deposited 2018-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S | MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.2 M sodium chloride 0.1 M Tris-HCl 8.0 20 % w/v PEG 6000
|
Resolution 1.63 Å R-free 0.200 |
| 6Q9I Aspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in complex with Factor X peptide fragment (39mer-4Ser) Deposited 2018-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S | FMT FORMIC ACID × 3 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M sodium formate, 20 % w/v PEG 3350
|
Resolution 1.85 Å R-free 0.223 |
| 6YYW Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 2-oxoglutarate, and factor X substrate peptide fragment(39mer-4Ser) Deposited 2020-05-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；100 mM Bis Tris Propane, 200 mM sodium acetate trihydrate, 20% w/v PEG 3350, 1 mM manganese chloride, 2 mM 2-oxoglutarate, 18 mg/ml protein
|
Resolution 2.27 Å R-free 0.224 |
| 6YYX Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 3-methyl-2-oxoglutarate, and factor X substrate peptide fragment(39mer-4Ser) Deposited 2020-05-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 Q1Z (3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；200 mM Bis Tris Propane, 200 mM sodium/potassium phosphate, 20% w/v PEG 3350, 1 mM manganese chloride, 2 mM 3-methyl-2-oxoglutarate, 18 mg/ml protein
|
Resolution 1.53 Å R-free 0.192 |
| 6YYY Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 4,4-dimethyl-2-oxoglutarate, and factor X substrate peptide fragment(39mer-4Ser) Deposited 2020-05-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 Q1W 2,2-dimethyl-4-oxidanylidene-pentanedioic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；200 mM sodium bromide, 20% w/v PEG 3350, 1 mM manganese chloride, 2 mM 4,4-dimethyl-2-oxoglutarate, 18 mg/ml protein
|
Resolution 2.29 Å R-free 0.244 |
| 6Z6Q Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 3-ethyl-2-oxoglutarate, and factor X substrate peptide fragment(39mer-4Ser) Deposited 2020-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Not recorded | GOL GLYCEROL × 1 MN MANGANESE (II) ION × 1 QA8 (3~{R})-3-ethyl-2-oxidanylidene-pentanedioic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；100 mM HEPES sodium, 200 mM ammonium chloride, 20% w/v PEG 6000, 1 mM manganese chloride, 2 mM 3-ethyl-2-oxoglutarate, 18 mg/ml protein
|
Resolution 1.81 Å R-free 0.232 |
| 6Z6R Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, N-oxalyl-alpha-methylalanine, and factor X substrate peptide fragment(39mer-4Ser) Deposited 2020-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 BR BROMIDE ION × 1 GOL GLYCEROL × 1 UQK N-oxalyl-alpha-methylalanine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM Bis Tris propane, 200 mM sodium bromide, 20% w/v PEG 3350, 1 mM manganese chloride, 2 mM N-oxalyl-alpha-methylalanine, 18 mg/ml protein
|
Resolution 2.13 Å R-free 0.242 |
| 7AHU Anti-FX Fab of mim8 in complex with human FXa Deposited 2020-09-25 | 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 C
235–475（241 aa）
Chain D
126–182（57 aa）
|
Not recorded | 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.2 M sodium acetate, 0.1 M sodium cacodylate, pH 6.5, 18 % (w/v) PEG 8000
|
Resolution 2.60 Å R-free 0.263 |
| 7AHU Anti-FX Fab of mim8 in complex with human FXa Deposited 2020-09-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
235–475（241 aa）
Chain F
126–182（57 aa）
|
Not recorded | 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.2 M sodium acetate, 0.1 M sodium cacodylate, pH 6.5, 18 % (w/v) PEG 8000
|
Resolution 2.60 Å R-free 0.263 |
| 7BMI Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 3-fluoropyridine-2,4-dicarboxylic acid, and factor X substrate peptide fragment (39mer-4Ser) Deposited 2021-01-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 U4B 3-fluoranylpyridine-2,4-dicarboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；100 mM HEPES sodium, 200 mM ammonium chloride, 20% w/v PEG 4000, 1 mM manganese chloride, 2 mM 2-oxoglutarate, 18 mg/ml protein
|
Resolution 1.66 Å R-free 0.220 |
| 7BMJ Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 5-fluoropyridine-2,4-dicarboxylic acid, and factor X substrate peptide fragment (39mer-4Ser) Deposited 2021-01-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 U4Q 5-fluoranylpyridine-2,4-dicarboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；200 mM sodium nitrate, 20% w/v PEG 3350, 1 mM manganese chloride, 18 mg/ml protein
|
Resolution 1.75 Å R-free 0.251 |
| 7E6J Aspartyl/Asparaginyl beta-hydroxylase (AspH) H725A in complex with Factor X peptide fragment (39mer-4Ser) Deposited 2021-02-22 | 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 B
86–124（39 aa）
|
Mutation：C90S,C95S,C112S,C121S | GOL GLYCEROL × 3 PPI PROPANOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；100mM PCTP, 25% w/v PEG 1500
|
Resolution 1.90 Å R-free 0.213 |
| 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 A
41–179（139 aa）
Fragment：UNP residues 41-179
Chain B
235–488（254 aa）
Fragment：UNP residues 235-488
|
Mutation：S379A | 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 |
| 7YB9 Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with L-2-hydroxyglutarate and factor X-derived peptide (39mer-4Ser) Deposited 2022-06-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S | MN MANGANESE (II) ION × 1 S2G (2S)-2-HYDROXYPENTANEDIOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M lithium chloride, 20 % w/v Polyethylene glycol 6,000, 0.1 M Bis-Tris propane
|
Resolution 1.54 Å R-free 0.215 |
| 7YBB Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with D-4-hydroxy-2-oxoglutarate and factor X-derived peptide (39mer-4Ser) Deposited 2022-06-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 IO9 (2~{R})-2-oxidanyl-4-oxidanylidene-pentanedioic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.02 M Sodium/potassium phosphate, 20 % w/v Polyethylene glycol 3,350, 0.1 M Bis-Tris propane
|
Resolution 1.68 Å R-free 0.219 |
| 7YBC Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with (S)-4-hydroxy-4-methyl-2-oxoglutarate and factor X-derived peptide (39mer-4Ser) Deposited 2022-06-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S | MN MANGANESE (II) ION × 1 GOL GLYCEROL × 1 IOW (2~{S})-2-methyl-2-oxidanyl-4-oxidanylidene-pentanedioic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2 M Sodium acetate trihydrate, 20 % w/v Polyethylene glycol 3,350, 0.1 M Bis Tris propane
|
Resolution 1.84 Å R-free 0.199 |
| 8EOK Structure of the C3bB proconvertase in complex with lufaxin and factor Xa Deposited 2022-10-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain C
235–488（254 aa）
Chain L
46–179（134 aa）
|
Not recorded | MG MAGNESIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.53 Å |
| 8RE5 Aspartyl/Asparaginyl beta-hydroxylase (AspH) R735Q variant in complex with Mn, 2-oxosuberate and a Factor X derived peptide fragment Deposited 2023-12-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S | YQX 2-oxidanylideneoctanedioic acid × 2 MN MANGANESE (II) ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M bis tris propane pH 7.5, 0.2 M NaBr, 20% PEG 3350
|
Resolution 1.70 Å R-free 0.207 |
| 8RE6 Aspartyl/Asparaginyl beta-hydroxylase (AspH) R735Q variant in complex with Mn, 2-oxoglutarate and a Factor X derived peptide fragment Deposited 2023-12-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S | MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 0.2 M NaCl, 20% PEG 3350
|
Resolution 1.92 Å R-free 0.216 |
| 8RE7 Aspartyl/Asparaginyl beta-hydroxylase (AspH) R735W variant in complex with Mn, 2-oxoglutarate and a Factor X derived peptide fragment Deposited 2023-12-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S | AKG 2-OXOGLUTARIC ACID × 1 MN MANGANESE (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 0.2 M NaCl, 20% PEG 3350
|
Resolution 1.95 Å R-free 0.242 |
| 8RE8 Aspartyl/Asparaginyl beta-hydroxylase (AspH) R688Q variant in complex with Mn, (3R)-methyl-2-oxoglutarate and a Factor X derived peptide fragment Deposited 2023-12-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S | Q1Z (3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 5 MN MANGANESE (II) ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 0.2 M NaCl, 20% PEG 3350
|
Resolution 1.85 Å R-free 0.208 |
| 8RE9 Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Mn, 2-oxoglutarate and a Factor X derived peptide fragment Deposited 2023-12-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S | AKG 2-OXOGLUTARIC ACID × 1 MN MANGANESE (II) ION × 1 PEG DI(HYDROXYETHYL)ETHER × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5 20 % v/v PEG Smear High (BCS screen)
|
Resolution 1.84 Å R-free 0.196 |
| 9BVL Vitamin K-dependent gamma-carboxylase with factor X propeptide and glutamate-rich region and with vitamin K hydroquinone Deposited 2024-05-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
22–85（64 aa）
Fragment：residues 22-85
|
Not recorded | A1AVC vitamin K1 hydroquinone × 1 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9CLI Cryo-EM model derived from localized reconstruction of human adenovirus (Ad5)-hexon-FX complex at 3.6A 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
1–488（488 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 3.61 Å |
| 9CM2 Cryo-EM model derived from localized reconstruction of human adenovirus 6-hexon-FX complex at 4.3A resolution 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
1–488（488 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CA CALCIUM ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.01 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 B
41–182（142 aa）
Chain C
235–469（235 aa）
|
Mutation：S195A | 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 |
| 9FVU Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate, thiocyanate and Factor X derived peptide fragment Deposited 2024-06-28 | 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 B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S | AKG 2-OXOGLUTARIC ACID × 1 FE FE (III) ION × 1 PEG DI(HYDROXYETHYL)ETHER × 8 SCN THIOCYANATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；0.1 M bis tris propane pH 7.5, 0.2 M NaSCN, 20% PEG 3350
|
Resolution 1.70 Å R-free 0.187 |
| 9FVV Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Mn, 2OG, thiocyanate and Factor X peptide fragment (39mer-4Ser) Deposited 2024-06-28 | 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 B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S | AKG 2-OXOGLUTARIC ACID × 1 ACT ACETATE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1 MN MANGANESE (II) ION × 1 SCN THIOCYANATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；0.1 M bis tris propane pH 7.5, 0.2 M NaSCN, 20% PEG 3350
|
Resolution 1.60 Å R-free 0.191 |
| 9FVW Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2OG, SIN and hydroxylated product of Factor X peptide fragment (39mer-4Ser) Deposited 2024-06-28 | 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 B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S Non-standard monomer：Yes (specific site not provided by mmCIF) | SIN SUCCINIC ACID × 1 AKG 2-OXOGLUTARIC ACID × 1 FE FE (III) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；0.1 M bis tris propane pH 7.5, 0.2 M NaBr, 20% PEG 3350
|
Resolution 1.90 Å R-free 0.224 |
| 9FVX Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate and Factor X derived peptide fragment Deposited 2024-06-28 | 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 B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S | AKG 2-OXOGLUTARIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 7 CL CHLORIDE ION × 2 FE FE (III) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；0.1 M bis tris propane pH 7.5, 0.2 M NaBr, 20% PEG 3350
|
Resolution 1.90 Å R-free 0.212 |
| 9FVY Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate, succinate and the hudroxylated product of Factor X derived peptide fragment after O2 exposure Deposited 2024-06-28 | 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 B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S Non-standard monomer：Yes (specific site not provided by mmCIF) | AKG 2-OXOGLUTARIC ACID × 1 SIN SUCCINIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 2 FE FE (III) ION × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；0.1 M bis tris propane pH 7.5, 0.2 M NaBr, 20% PEG 3350
|
Resolution 1.90 Å R-free 0.199 |
| 9FVZ Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate and a Factor X derived peptide fragment Deposited 2024-06-28 | 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 B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S | AKG 2-OXOGLUTARIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 6 GOL GLYCEROL × 1 FE FE (III) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；0.1 M bis tris propane pH 7.5, 0.2 M NaBr, 20% PEG 3350
|
Resolution 1.98 Å R-free 0.213 |
| 9FW0 Room temperature structure of Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate and Factor X derived peptide fragment Deposited 2024-06-28 | 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 B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S | AKG 2-OXOGLUTARIC ACID × 1 FE FE (III) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 7.5；278 K；16% PEG 3350, 0.1 M Bis Tris propane pH 7.5, 0.1 M KSCN
|
Resolution 1.95 Å R-free 0.207 |
| 9HNZ Room temperature structure of Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate and hydroxylated Factor X derived peptide fragment, 2 h O2 exposure Deposited 2024-12-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S Non-standard monomer：Yes (specific site not provided by mmCIF) | SIN SUCCINIC ACID × 1 FE FE (III) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 7.5；278 K；16% PEG3350, 0.1 M bis tris propane pH 7.5, 0.1 M KSCN
|
Resolution 2.40 Å R-free 0.237 |
| 9HO0 Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate, succinate and the hydroxylated product of Factor X derived peptide fragment, 12 h O2 exposure Deposited 2024-12-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S Non-standard monomer：Yes (specific site not provided by mmCIF) | SIN SUCCINIC ACID × 1 FE FE (III) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 7.5；278 K；16% PEG 3350, 0.1 M bis-tris propane pH 7.5, 0.1 M KSCN
|
Resolution 2.14 Å R-free 0.232 |
| 9HO1 Room temperature structure of Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate, and hydroxylated Factor X derived peptide fragment, 1.5 s O2 exposure Deposited 2024-12-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S Non-standard monomer：Yes (specific site not provided by mmCIF) | AKG 2-OXOGLUTARIC ACID × 1 SIN SUCCINIC ACID × 1 FE FE (III) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 7.5；278 K；16% PEG3350, 0.1M Bis Tris propane pH 7.5, 0.1 M KSCN
|
Resolution 1.85 Å R-free 0.221 |
| 9HO2 Room temperature structure of Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate and Factor X derived peptide fragment, excess Fe removed Deposited 2024-12-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S | AKG 2-OXOGLUTARIC ACID × 1 FE FE (III) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 7.5；278 K；16% PEG 3350, 0.1 M Bis Tris propane pH 7.5, 0.1 M KSCN
|
Resolution 1.83 Å R-free 0.219 |
| 9HO3 Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2OG, nitric oxide, and Factor X peptide fragment Deposited 2024-12-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
86–124（39 aa）
|
Mutation：C90S, C95S, C112S, C121S | NA SODIUM ION × 1 K POTASSIUM ION × 1 FE FE (III) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 NO NITRIC OXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；0.1 M bis tris propane pH 7.5, 16% PEG3350, 0.1 M KSCN
|
Resolution 2.39 Å R-free 0.242 |
| 9I24 Coagulation factor Xa complex with a2-loop peptide Deposited 2025-01-17 | 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
235–486（252 aa）
Chain L
126–179（54 aa）
|
Not recorded | CA CALCIUM ION × 1 NA SODIUM ION × 1 CL CHLORIDE ION × 1 IMD IMIDAZOLE × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；287 K；imidazole, MPD
|
Resolution 1.20 Å R-free 0.172 |
| 9I2H A 3.3 angstrom cryo-EM structure of an engineered high-affinity human prothrombinase complex Deposited 2025-01-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: pentameric |
Chain H
235–488（254 aa）
Chain L
41–179（139 aa）
|
Mutation：E129N, S130E, T132K, K134D, N166H, K169M, S173D, I175R, A233R, D239K Mutation：S90R, L91A, D92F, H101K, E102R, E103V, N105S | CA CALCIUM ION × 2 NA SODIUM ION × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 1 CU COPPER (II) ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20mM HEPES, 150mM NaCl and 5mM CaCl2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.28 Å |
| 9L6S double-mutant (K217A & K218A) Vitamin K-dependent gamma-carboxylase in complex with coagulation factors X and vitamin K Deposited 2024-12-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–488（488 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 A1EMC 2-methyl-3-[(2~{E},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]naphthalene-1,4-diol × 1 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 2 CLR CHOLESTEROL × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.58 Å |
| 9P0X Nanodisc-embedded human TF/FVIIa/XK1 in complex with 10H10 Fab (nanodisc-subtracted) Deposited 2025-06-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric |
Chain X
41–171（131 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 4 CA CALCIUM ION × 12 BGC beta-D-glucopyranose × 1 FUC alpha-L-fucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 9R8R Factor Xa bound to BAY 3389934 Deposited 2025-05-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
235–468（234 aa）
Chain B
128–177（50 aa）
|
Not recorded | CA CALCIUM ION × 1 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 GOL GLYCEROL × 2 PE8 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；0.1M MES pH5.8, 3.5% PEG1000, 25% PEG600, 11% Glycerol
|
Resolution 2.04 Å R-free 0.266 |
| 9WF9 Cryo-EM structure of GGCX-FX complex Deposited 2025-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
23–50（28 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 2 MX7 (2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate × 1 CLR CHOLESTEROL × 1 A1AT1 (1aR,7aS)-1a-methyl-7a-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]-1a,7a-dihydronaphtho[2,3-b]oxirene-2,7-dione × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.83 Å |
| 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 E
124–467（344 aa）
|
Mutation：S379A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.84 Å |
183 other PDB entries and 220 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | FA10_HUMAN |
| Isoform | — |
| PDB entities | 1, 2 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–234； UniProt 235–468 Author chain B； PDBConstruct 1–51； UniProt 128–178 |
