MolNFT v1 · #15801 · protein
Crystal structure of human coagulation factor xa complexed with RPR208944
1NFX · Coagulation factor xa, heavy chain: “Crystal structure of human coagulation factor xa complexed with RPR208944”. X-ray diffraction, 2 ligands (RDR, CA), 3 pockets (best druggability 0.48). MolNFT v1 #15801 on GenesisL1: 3D…
- PDB
- 1NFX
- Type
- protein
- Length
- 287 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
- RDR, CA
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 13% 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, 38% strand | P00742 |
| B | Coagulation factor xa, light chain (EC 3.4.21.6) | protein | 53 | 13% helix, 30% strand | P00742 |
Ligands and binding sites
- 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 · 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 | 126 | 0.48 | 0.79 | 30 | RDR |
| 2 | 56 | 0.37 | 0.80 | 22 | empty |
| 3 | 83 | 0.36 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 958 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1NFX · Crystal structure of human coagulation factor xa complexed with RPR208944 · 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 1NFX · PDBe 1NFX · UniProt P00742
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