Research workbench
Factor xa in complex with D102-4380
Analyse Factor xa in complex with D102-4380 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TK5
- Type
- protein
- Length
- 287 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Factor X heavy chain; Factor X light chain
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- D1Q, CA
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Factor X heavy chain (EC 3.4.21.6) | protein | 233 | 13% helix, 37% strand | P00742 |
| B | Factor X light chain (EC 3.4.21.6) | protein | 54 | 13% helix, 30% strand | P00742 |
Ligands and binding sites
- D1Q · 4-{3-[(4-chlorophenyl)amino]-3-oxopropyl}-3-({[5-(propan-2-yl)-4,5,6,7-tetrahydro[1,3]thiazolo[5,4-c]pyridin-2-yl]carbonyl}amino)benzoic acid · ligand · chains A
- CA · Calcium ion · metal · 2 copies · 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 | 132 | 0.47 | 0.78 | 30 | D1Q |
| 2 | 90 | 0.38 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 888 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 3TK5 · PDBe 3TK5 · UniProt P00742
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