Research workbench
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
Analyse X-ray crystal structure of human fxa in complex with (S)-N-((2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K9X
- Type
- protein
- Length
- 643 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (coagulation factor X)
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- MBM, CA, NA
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (coagulation factor X) (EC 3.4.21.6) | protein | 86 | 5% helix, 30% strand | P00742 |
| B, D | Protein (coagulation factor X) (EC 3.4.21.6) | protein | 238 | 13% helix, 36% strand | P00742 |
| C | Protein (coagulation factor X) (EC 3.4.21.6) | protein | 81 | 5% helix, 32% strand | P00742 |
Ligands and binding sites
- 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 · ligand · 2 copies · chains B, A, D
- CA · Calcium ion · metal · 2 copies · chains B, D
- NA · Sodium ion · metal · 2 copies · chains B, D
- GOL · Glycerol · additive · 6 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.74 | 0.82 | 45 | MBM |
| 2 | 664 | 0.72 | 0.79 | 69 | GOL |
| 3 | 125 | 0.44 | 0.77 | 26 | GOL |
| 4 | 121 | 0.44 | 0.77 | 29 | MBM |
| 5 | 65 | 0.32 | 0.75 | 16 | GOL |
Interfaces
4 interfaces between chains.
- A–B · 923 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 917 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 849 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 371 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 21 disulfide (disulfide).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00742
- Elsewhere: RCSB PDB 3K9X · PDBe 3K9X · UniProt P00742
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