Research workbench
Crystal structure of a human factor xa inhibitor complex
Analyse Crystal structure of a human factor xa inhibitor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J4I
- Type
- protein
- Length
- 284 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
- GSJ, CA
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor X (EC 3.4.21.6) | protein | 232 | 14% helix, 38% strand | P00742 |
| B | Coagulation factor X (EC 3.4.21.6) | protein | 52 | 13% helix, 31% strand | P00742 |
Ligands and binding sites
- GSJ · 1-pyrrolidineacetamide, 3-[[(6-chloro-2-naphthalenyl)sulfonyl]amino]-alpha-methyl-N-(1-methylethyl)-N-[2-[(methylsulfonyl)amino]ethyl]-2-oxo-, (alphas,3s)- · 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 | 175 | 0.48 | 0.76 | 28 | empty |
| 2 | 108 | 0.46 | 0.79 | 23 | GSJ |
Interfaces
1 interface between chains.
- A–B · 925 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 2J4I · PDBe 2J4I · UniProt P00742
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