MolNFT v1 · #40770 · protein
Crystal structure of a human factor xa inhibitor complex
2J38 · Activated factor xa heavy chain: “Crystal structure of a human factor xa inhibitor complex”. X-ray diffraction, 2 ligands (GS5, CA), 2 pockets (best druggability 0.47). MolNFT v1 #40770 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2J38
- Type
- protein
- Length
- 285 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
- GS5, CA
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activated factor xa heavy chain (EC 3.4.21.6) | protein | 234 | 13% helix, 36% strand | P00742 |
| B | Factor X light chain (EC 3.4.21.6) | protein | 51 | 14% helix, 27% strand | P00742 |
Ligands and binding sites
- GS5 · 5-chloro-N-{(3S)-1-[(1S)-1-methyl-2-morpholin-4-yl-2-oxoethyl]-2-oxopyrrolidin-3-yl}-1-benzothiophene-2-sulfonamide · 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 | 183 | 0.47 | 0.75 | 30 | empty |
| 2 | 110 | 0.46 | 0.79 | 22 | GS5 |
Interfaces
1 interface between chains.
- A–B · 896 Ų buried · 11 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 2J38 · PDBe 2J38 · UniProt P00742
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