MolNFT v1 · #153865 · protein
Structure of geobacillus kaustophilus lactonase, Y99P/D266N double mutant with bound 3-oxo-C8-hsl
6JST · Phosphotriesterase: “Structure of geobacillus kaustophilus lactonase, Y99P/D266N double mutant with bound 3-oxo-C8-hsl”. X-ray diffraction, 4 ligands (LAE, FE, ZN), 9 pockets (best druggability 0.75). MolNFT v1 #153865 on GenesisL1…
- PDB
- 6JST
- Type
- protein
- Length
- 1,292 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotriesterase
- EC
- 3.5.-.-
- UniProt
- Q5KZU5
- Ligands
- LAE, FE, ZN, OH
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phosphotriesterase (EC 3.5.-.-) | protein | 323 | 47% helix, 16% strand | Q5KZU5 |
Ligands and binding sites
- LAE · 3-oxo-octanoic acid (2-oxo-tetrahydro-furan-3-yl)-amide · ligand · chains A, B
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- OH · Hydroxide ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.75 | 0.78 | 110 | ZN |
| 2 | 454 | 0.74 | 0.83 | 65 | OH, LAE |
| 3 | 213 | 0.71 | 0.87 | 33 | OH |
| 4 | 446 | 0.68 | 0.80 | 57 | OH |
| 5 | 646 | 0.65 | 0.75 | 67 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1766 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1718 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 44 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 6JST · Structure of Geobacillus kaustophilus lactonase, Y99P/D266N double mutant with bound… · the same entry in another collection · chain A 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 Q5KZU5
- Elsewhere: RCSB PDB 6JST · PDBe 6JST · UniProt Q5KZU5
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