Research workbench
Factor xa in complex with the dual thrombin-fxa inhibitor 31.
Analyse Factor xa in complex with the dual thrombin-fxa inhibitor 31. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BTT
- Type
- protein
- Length
- 571 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor X light chain; Coagulation factor X
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- VYR, CA
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor X light chain (EC 3.4.21.6) | protein | 51 | 8% helix, 31% strand | P00742 |
| B, F | Coagulation factor X (EC 3.4.21.6) | protein | 234 | 13% helix, 37% strand | P00742 |
| E | Coagulation factor X light chain (EC 3.4.21.6) | protein | 52 | 8% helix, 27% strand | P00742 |
Ligands and binding sites
- VYR · N-[(S)-1-[5-(5-Chloro-thiophen-2-yl)-isoxazol-3-ylmethyl]-2-(4-methoxy-piperidin-1-yl)-2-oxo-ethyl]-2-ethyl-3-(3-oxo-morpholin-4-yl)-benzenesulfonamide · ligand · 2 copies · chains B, F
- CA · Calcium ion · metal · 2 copies · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.72 | 0.76 | 98 | empty |
| 2 | 201 | 0.54 | 0.78 | 40 | VYR |
| 3 | 168 | 0.49 | 0.77 | 29 | empty |
| 4 | 130 | 0.48 | 0.79 | 24 | VYR |
| 5 | 57 | 0.34 | 0.78 | 16 | empty |
Interfaces
5 interfaces between chains.
- E–F · 900 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 869 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 334 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 242 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 143 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 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 4BTT · PDBe 4BTT · UniProt P00742
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