MolNFT v1 · #53088 · protein
Structure of holo form of vibrio cholerae cqsa
2WK8 · Cai-1 autoinducer synthase: “Structure of holo form of vibrio cholerae cqsa”. X-ray diffraction, 2 ligands (PLP, SO4), 8 pockets (best druggability 0.77). MolNFT v1 #53088 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2WK8
- Type
- protein
- Length
- 746 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cai-1 autoinducer synthase
- EC
- 2.3.-.-
- UniProt
- Q9KM65
- Ligands
- PLP, SO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cai-1 autoinducer synthase (EC 2.3.-.-) | protein | 382 | 45% helix, 15% strand | Q9KM65 |
| B | Cai-1 autoinducer synthase (EC 2.3.-.-) | protein | 364 | 44% helix, 16% strand | Q9KM65 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.77 | 0.89 | 54 | PLP |
| 2 | 886 | 0.76 | 0.80 | 100 | PLP |
| 3 | 63 | 0.74 | 0.98 | 18 | empty |
| 4 | 324 | 0.64 | 0.80 | 43 | empty |
| 5 | 101 | 0.57 | 0.85 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3456 Ų buried · 29 hydrogen bonds · protein-protein
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 Q9KM65
- Elsewhere: RCSB PDB 2WK8 · PDBe 2WK8 · UniProt Q9KM65
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