Research workbench
Crystal structure of Brevundimonas diminuta phosphotriesterase mutant L7eP-3a
Analyse Crystal structure of Brevundimonas diminuta phosphotriesterase mutant L7eP-3a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZST
- Type
- protein
- Length
- 658 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.011
- Source
- Brevundimonas diminuta
- Molecule
- Parathion hydrolase
- EC
- 3.1.8.1
- UniProt
- P0A434
- Ligands
- CO
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · resolution 2.011 · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Parathion hydrolase (EC 3.1.8.1) | protein | 329 | 52% helix, 15% strand | P0A434 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.62 | 0.85 | 34 | empty |
| 2 | 176 | 0.56 | 0.80 | 28 | empty |
| 3 | 147 | 0.55 | 0.81 | 25 | CO |
| 4 | 54 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1405 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 4ZST · Crystal structure of brevundimonas diminuta phosphotriesterase mutant L7EP-3A · the same entry in another collection · chain A against A, TM-score 1.00
- P0A434 · AlphaFold monomer V2.0 prediction for parathion hydrolase (P0A434) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0A434
- Elsewhere: RCSB PDB 4ZST · PDBe 4ZST · UniProt P0A434
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