MolNFT v1 · #6048 · protein
Crystal structure of human coagulation factor xa complexed with RPR208815
1F0R: “Crystal structure of human coagulation factor xa complexed with RPR208815”. X-ray diffraction, 2 ligands (815, CA), 2 pockets (best druggability 0.48). MolNFT v1 #6048 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1F0R
- Type
- protein
- Length
- 285 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor xa
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- 815, CA
- Pockets
- 2 · 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 (EC 3.4.21.6) | protein | 234 | 14% helix, 38% strand | P00742 |
| B | Coagulation factor xa (EC 3.4.21.6) | protein | 51 | 8% helix, 31% strand | P00742 |
Ligands and binding sites
- 815 · Thieno[3,2-b]pyridine-2-sulfonic acid [1-(1-amino-isoquinolin-7-ylmethyl)-2-oxo-pyrroldin-3-yl]-amide · 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
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.48 | 0.79 | 25 | 815 |
| 2 | 128 | 0.44 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 936 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1F0R · Crystal structure of human coagulation factor xa complexed with RPR208815 · 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 1F0R · PDBe 1F0R · UniProt P00742
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