Research workbench
Factor xa complex with GTC000401
Analyse Factor xa complex with GTC000401 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y76
- Type
- protein
- Length
- 285 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
- 4O1, CA
- Pockets
- 2 · best druggability 0.48
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 | 232 | 13% helix, 36% strand | P00742 |
| B | Coagulation factor X (EC 3.4.21.6) | protein | 53 | 13% helix, 30% strand | P00742 |
Ligands and binding sites
- 4O1 · N~2~-[(6-chloronaphthalen-2-yl)sulfonyl]-N~2~-{(3S)-1-[(2S)-1-(4-methyl-1,4-diazepan-1-yl)-1-oxopropan-2-yl]-2-oxopyrrolidin-3-yl}glycinamide · 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 | 203 | 0.48 | 0.75 | 29 | empty |
| 2 | 102 | 0.45 | 0.79 | 23 | 4O1 |
Interfaces
1 interface between chains.
- A–B · 891 Ų buried · 10 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 4Y76 · PDBe 4Y76 · UniProt P00742
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