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Structure of geobacillus kaustophilus lactonase, mutant E101G/R230C/D266N with ZN2+ and bound N-butyryl-dl-homoserine lactone
Analyse Structure of geobacillus kaustophilus lactonase, mutant E101G/R230C/D266N with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H9X
- Type
- protein
- Length
- 636 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotriesterase
- EC
- 3.5.-.-
- UniProt
- Q5KZU5
- Ligands
- HL4, FE, ZN, OH
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphotriesterase (EC 3.5.-.-) | protein | 318 | 47% helix, 18% strand | Q5KZU5 |
Ligands and binding sites
- HL4 · N-[(3S)-2-oxotetrahydrofuran-3-yl]butanamide · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- OH · Hydroxide ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.76 | 0.83 | 55 | ZN, OH, HL4 |
| 2 | 474 | 0.75 | 0.83 | 57 | ZN, OH, HL4 |
| 3 | 508 | 0.61 | 0.75 | 43 | empty |
| 4 | 237 | 0.60 | 0.80 | 24 | empty |
| 5 | 72 | 0.38 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1729 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 4H9X · Structure of Geobacillus kaustophilus lactonase, mutant E101G/R230C/D266N with Zn2+ and… · 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 4H9X · PDBe 4H9X · UniProt Q5KZU5
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