Research workbench
Structure of an engineered organophosphorous hydrolase with increased activity toward hydrolysis of phosphothiolate bonds
Analyse Structure of an engineered organophosphorous hydrolase with increased activity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QW7
- Type
- protein
- Length
- 672 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Parathion hydrolase
- EC
- 3.1.8.1
- UniProt
- P0A434
- Ligands
- EBP, CO, NA
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Parathion hydrolase (EC 3.1.8.1) | protein | 336 | 50% helix, 15% strand | P0A434 |
Ligands and binding sites
- EBP · Diethyl 4-methylbenzylphosphonate · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.70 | 0.89 | 32 | empty |
| 2 | 197 | 0.60 | 0.82 | 30 | empty |
| 3 | 202 | 0.59 | 0.81 | 33 | empty |
| 4 | 70 | 0.34 | 0.76 | 16 | empty |
| 5 | 72 | 0.33 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1348 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 1QW7 · Structure of an Engineered Organophosphorous Hydrolase with Increased Activity Toward… · 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 1QW7 · PDBe 1QW7 · UniProt P0A434
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