MolNFT v1 · #32310 · protein
Crystal structure of factor xa in complex with 50
2BMG · Coagulation factor X: “Crystal structure of factor xa in complex with 50”. X-ray diffraction, 2 ligands (I1H, CA), 3 pockets (best druggability 0.46). MolNFT v1 #32310 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2BMG
- Type
- protein
- Length
- 287 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor X
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- I1H, CA
- Pockets
- 3 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor X (EC 3.4.21.6) | protein | 53 | 8% helix, 26% strand | P00742 |
| B | Coagulation factor X (EC 3.4.21.6) | protein | 234 | 14% helix, 37% strand | P00742 |
Ligands and binding sites
- I1H · 3-[2-(2,4-dichlorophenyl)ethoxy]-4-methoxy-N-[(1-pyridin-4-ylpiperidin-4-yl)methyl]benzamide · ligand · chains B
- CA · Calcium ion · metal · chains B
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 | 110 | 0.46 | 0.79 | 24 | I1H |
| 2 | 130 | 0.45 | 0.77 | 27 | empty |
| 3 | 50 | 0.27 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 899 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
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 2BMG · PDBe 2BMG · UniProt P00742
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