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Structure of PLP_THR aldimine form of vibrio cholerae cqsa
Analyse Structure of PLP_THR aldimine form of vibrio cholerae cqsa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WK9
- Type
- protein
- Length
- 762 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, PLG, SO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cai-1 autoinducer synthase (EC 2.3.-.-) | protein | 382 | 44% helix, 16% strand | Q9KM65 |
| B | Cai-1 autoinducer synthase (EC 2.3.-.-) | protein | 380 | 46% helix, 16% strand | Q9KM65 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A, B
- PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.78 | 0.90 | 57 | PLG |
| 2 | 304 | 0.76 | 0.88 | 56 | PLP |
| 3 | 532 | 0.74 | 0.82 | 78 | empty |
| 4 | 63 | 0.73 | 0.98 | 19 | empty |
| 5 | 149 | 0.67 | 0.87 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 3892 Ų buried · 32 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 2WK9 · PDBe 2WK9 · UniProt Q9KM65
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