Research workbench
Structure of Geobacillus kaustophilus lactonase, wild-type with Zn2+
Analyse Structure of Geobacillus kaustophilus lactonase, wild-type with Zn2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H9U
- Type
- protein
- Length
- 646 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.099
- Source
- Geobacillus kaustophilus
- Molecule
- Phosphotriesterase
- EC
- 3.5.-.-
- UniProt
- Q5KZU5
- Ligands
- FE, ZN, OH
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.099 · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphotriesterase (EC 3.5.-.-) | protein | 323 | 46% helix, 16% strand | Q5KZU5 |
Ligands and binding sites
- 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.75 | 0.78 | 141 | OH, ZN |
| 2 | 87 | 0.40 | 0.77 | 13 | empty |
| 3 | 72 | 0.35 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1706 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 4H9U · Structure of geobacillus kaustophilus lactonase, wild-type with ZN2+ · 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 4H9U · PDBe 4H9U · UniProt Q5KZU5
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