MolNFT v1 · #54011 · protein
Factor xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor
2XC0 · Activated factor xa heavy chain: “Factor xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor”. X-ray diffraction, 3 ligands (8NC, CA, NA), 2 pockets (best druggability 0.47). MolNFT v1 #54011 on GenesisL1: 3D structure…
- PDB
- 2XC0
- Type
- protein
- Length
- 278 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Activated factor xa heavy chain; Factor X light chain
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- 8NC, CA, NA
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activated factor xa heavy chain (EC 3.4.21.6) | protein | 234 | 14% helix, 36% strand | P00742 |
| L | Factor X light chain (EC 3.4.21.6) | protein | 44 | 9% helix, 18% strand | P00742 |
Ligands and binding sites
- 8NC · (3R,4R)-1-methanesulfonyl-pyrrolidine-3,4--dicarboxylic acid 3-[(3-fluoro-4-methoxy-phenyl)-amide] 4-{[2-fluoro-4-(2-oxo-2H-pyridin-1-yl)-phenyl]-amide} · ligand · chains A
- CA · Calcium ion · metal · chains A
- NA · Sodium 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 | 151 | 0.47 | 0.77 | 27 | 8NC |
| 2 | 127 | 0.45 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–L · 906 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2XC0 · Factor Xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor · 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 2XC0 · PDBe 2XC0 · UniProt P00742
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.