MolNFT v1 · #19834 · protein
Structure of an engineered organophosphorous hydrolase with increased activity toward hydrolysis of phosphothiolate bonds
1QW7 · Parathion hydrolase: “Structure of an engineered organophosphorous hydrolase with increased activity toward hydrolysis of…”. X-ray diffraction, 3 ligands (EBP, CO, NA), 5 pockets (best druggability 0.70). MolNFT v1 #19834 on…
- 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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