MolNFT v1 · #6013 · protein
Crystal structure of human coagulation factor xa complexed with RPR128515
1EZQ: “Crystal structure of human coagulation factor xa complexed with RPR128515”. X-ray diffraction, 2 ligands (RPR, CA), 2 pockets (best druggability 0.46). MolNFT v1 #6013 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1EZQ
- 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
- RPR, CA
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor xa (EC 3.4.21.6) | protein | 234 | 14% helix, 36% strand | P00742 |
| B | Coagulation factor xa (EC 3.4.21.6) | protein | 51 | 20% helix, 24% strand | P00742 |
Ligands and binding sites
- RPR · 3-[(3'-aminomethyl-biphenyl-4-carbonyl)-amino]-2-(3-carbamimidoyl-benzyl)-butyric acid methyl ester · 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 | 102 | 0.46 | 0.80 | 23 | RPR |
| 2 | 167 | 0.46 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 921 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1EZQ · Crystal structure of human coagulation factor xa complexed with RPR128515 · 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 1EZQ · PDBe 1EZQ · UniProt P00742
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