Research workbench
Crystal structure of human coagulation factor xa complexed with RPR132747
Analyse Crystal structure of human coagulation factor xa complexed with RPR132747 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NFU
- Type
- protein
- Length
- 286 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.05
- Source
- Homo sapiens
- Molecule
- Coagulation factor xa, heavy chain; Coagulation factor xa, light chain
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- RRP, CA
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · resolution 2.05 · 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 | 12% helix, 38% strand | P00742 |
| B | Coagulation factor xa, light chain (EC 3.4.21.6) | protein | 52 | 13% helix, 31% strand | P00742 |
Ligands and binding sites
- RRP · 3-({4-[(6-chloro-1-benzothien-2-yl)sulfonyl]-2-oxopiperazin-1-yl}methyl)benzenecarboximidamide · 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 | 176 | 0.48 | 0.76 | 27 | empty |
| 2 | 92 | 0.45 | 0.80 | 19 | RRP |
Interfaces
1 interface between chains.
- A–B · 863 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1NFU · Crystal structure of human coagulation factor xa complexed with RPR132747 · 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 1NFU · PDBe 1NFU · UniProt P00742
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