MolNFT v1 · #53090 · protein
Structure of PLP_THR_DECANOYL-CoA aldimine form of vibrio cholerae cqsa
2WKA · Cai-1 autoinducer synthase: “Structure of PLP_THR_DECANOYL-CoA aldimine form of vibrio cholerae cqsa”. X-ray diffraction, 3 ligands (P89, SO4, CL), 10 pockets (best druggability 0.79). MolNFT v1 #53090 on GenesisL1: 3D structure…
- PDB
- 2WKA
- Type
- protein
- Length
- 766 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
- P89, SO4, CL
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cai-1 autoinducer synthase (EC 2.3.-.-) | protein | 386 | 45% helix, 15% strand | Q9KM65 |
| B | Cai-1 autoinducer synthase (EC 2.3.-.-) | protein | 380 | 46% helix, 16% strand | Q9KM65 |
Ligands and binding sites
- P89 · [6-methyl-5-oxidanyl-4-[(~{E})-2-oxidanylideneundecyliminomethyl]pyridin-3-yl]methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.79 | 0.89 | 60 | P89 |
| 2 | 363 | 0.76 | 0.87 | 55 | P89, CL |
| 3 | 547 | 0.74 | 0.82 | 83 | empty |
| 4 | 127 | 0.72 | 0.92 | 33 | empty |
| 5 | 98 | 0.69 | 0.92 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 3949 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 2WKA · Structure of Plp_Thr_decanoyl-CoA aldimine form of Vibrio cholerae CqsA · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KM65 · AlphaFold monomer V2.0 prediction for cai-1 autoinducer synthase (Q9KM65) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 2WKA · PDBe 2WKA · UniProt Q9KM65
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