MolNFT v1 · #153864 · protein
Structure of geobacillus kaustophilus lactonase, Y99P mutant
6JSS · Phosphotriesterase: “Structure of geobacillus kaustophilus lactonase, Y99P mutant”. X-ray diffraction, 3 ligands (FE, ZN, OH), 12 pockets (best druggability 0.74). MolNFT v1 #153864 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6JSS
- 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
- FE, ZN, OH
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phosphotriesterase (EC 3.5.-.-) | protein | 323 | 46% helix, 16% strand | Q5KZU5 |
Ligands and binding sites
- 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 · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.74 | 0.77 | 104 | OH |
| 2 | 288 | 0.72 | 0.85 | 42 | OH |
| 3 | 374 | 0.71 | 0.83 | 54 | OH |
| 4 | 411 | 0.69 | 0.81 | 58 | ZN, OH |
| 5 | 407 | 0.63 | 0.77 | 53 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1785 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1774 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 253 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 6JSS · Structure of Geobacillus kaustophilus lactonase, Y99P mutant · 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 6JSS · PDBe 6JSS · UniProt Q5KZU5
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