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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
Analyse Crystal structure of human fxa in complex with (S)-2-cyano-1-(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HPT
- Type
- protein
- Length
- 645 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor X
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- YET, CA, NA
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor X (EC 3.4.21.6) | protein | 84 | 5% helix, 29% strand | P00742 |
| B | Coagulation factor X (EC 3.4.21.6) | protein | 238 | 13% helix, 37% strand | P00742 |
| C | Coagulation factor X (EC 3.4.21.6) | protein | 86 | 5% helix, 28% strand | P00742 |
| D | Coagulation factor X (EC 3.4.21.6) | protein | 237 | 14% helix, 37% strand | P00742 |
Ligands and binding sites
- 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 · 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
- ACT · Acetate ion · additive · 8 copies · chains B, D, A
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains B, D
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.72 | 0.81 | 52 | YET |
| 2 | 548 | 0.69 | 0.79 | 55 | ACT |
| 3 | 210 | 0.51 | 0.76 | 29 | GOL, ACT |
| 4 | 115 | 0.46 | 0.79 | 25 | YET |
| 5 | 67 | 0.32 | 0.75 | 22 | GOL |
Interfaces
4 interfaces between chains.
- A–B · 923 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 836 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 687 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 383 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 22 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 3HPT · PDBe 3HPT · UniProt P00742
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