MolNFT v1 · #81458 · protein
Crystal structure of pte mutant H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/R67H
3URB · Parathion hydrolase: “Crystal structure of pte mutant H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/R67H”. X-ray diffraction, 2 ligands (DPF, CO), 5 pockets (best druggability 0.63). MolNFT v1 #81458 on GenesisL1: 3D…
- PDB
- 3URB
- Type
- protein
- Length
- 644 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
- DPF, CO
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Parathion hydrolase (EC 3.1.8.1) | protein | 321 | 52% helix, 14% strand | P0A434 |
| B | Parathion hydrolase (EC 3.1.8.1) | protein | 323 | 52% helix, 14% strand | P0A434 |
Ligands and binding sites
- DPF · Diethyl hydrogen phosphate · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B
- IMD · Imidazole · additive · 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 | 175 | 0.63 | 0.84 | 32 | IMD |
| 2 | 269 | 0.62 | 0.80 | 33 | DPF |
| 3 | 227 | 0.61 | 0.81 | 34 | DPF |
| 4 | 72 | 0.33 | 0.75 | 17 | empty |
| 5 | 60 | 0.32 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1491 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 3URB · Crystal Structure of PTE mutant H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V… · 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 P0A434
- Elsewhere: RCSB PDB 3URB · PDBe 3URB · UniProt P0A434
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