Research workbench
Crystal structure of human coagulation factor xa complexed with RPR209685
Analyse Crystal structure of human coagulation factor xa complexed with RPR209685 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NFW
- Type
- protein
- Length
- 285 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor xa, heavy chain; Coagulation factor xa, light chain
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- RRR, CA
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor xa, heavy chain (EC 3.4.21.6) | protein | 234 | 13% helix, 37% strand | P00742 |
| B | Coagulation factor xa, light chain (EC 3.4.21.6) | protein | 51 | 8% helix, 31% strand | P00742 |
Ligands and binding sites
- RRR · 4-{[(E)-2-(5-chlorothien-2-yl)vinyl]sulfonyl}-1-(1H-pyrrolo[3,2-c]pyridin-2-ylmethyl)piperazin-2-one · ligand · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.45 | 0.75 | 29 | empty |
| 2 | 89 | 0.44 | 0.80 | 20 | RRR |
| 3 | 52 | 0.33 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 947 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1NFW · Crystal structure of human coagulation factor xa complexed with RPR209685 · the same entry in another collection · chain A against A, TM-score 1.00
- P00742 · AlphaFold monomer V2.0 prediction for coagulation factor X (P00742) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 1NFW · PDBe 1NFW · UniProt P00742
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