MolNFT v1 · #17862 · protein
Crystal structure of phosphotriesterase triple mutant H254G/H257W/L303T complexed with diisopropylmethylphosphonate
1P6C · Parathion hydrolase: “Crystal structure of phosphotriesterase triple mutant H254G/H257W/L303T complexed with…”. X-ray diffraction, 3 ligands (EBP, DII, ZN), 6 pockets (best druggability 0.73). MolNFT v1 #17862 on GenesisL1: 3D…
- PDB
- 1P6C
- Type
- protein
- Length
- 661 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Parathion hydrolase
- EC
- 3.1.8.1
- UniProt
- P0A433
- Ligands
- EBP, DII, ZN
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Parathion hydrolase (EC 3.1.8.1) | protein | 331 | 50% helix, 14% strand | P0A433 |
| B | Parathion hydrolase (EC 3.1.8.1) | protein | 330 | 51% helix, 13% strand | P0A433 |
Ligands and binding sites
- EBP · Diethyl 4-methylbenzylphosphonate · ligand · 2 copies · chains A, B
- DII · Methylphosphonic acid diisopropyl ester · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.73 | 0.90 | 28 | empty |
| 2 | 271 | 0.63 | 0.81 | 37 | ZN, DII |
| 3 | 270 | 0.62 | 0.80 | 37 | ZN, DII |
| 4 | 84 | 0.40 | 0.78 | 17 | empty |
| 5 | 73 | 0.37 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1420 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 1P6C · crystal structure of phosphotriesterase triple mutant H254G/H257W/L303T complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A433 · AlphaFold monomer V2.0 prediction for parathion hydrolase (P0A433) · a predicted model of the same protein · 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 P0A433
- Elsewhere: RCSB PDB 1P6C · PDBe 1P6C · UniProt P0A433
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