› 3cak

X-ray diffraction
1.83Å resolution

X-ray structure of WT PTE with ethyl phosphate

Released:
DOI: 10.2210/pdb3cak/pdb
PDB entry 3cak coloured by chain, front view.
PDB entry 3cak coloured by chain, side view.
PDB entry 3cak coloured by chain, top view.
Source organism: Brevundimonas diminuta
Primary publication:
Structure of diethyl phosphate bound to the binuclear metal center of phosphotriesterase.
Kim J, Tsai PC, Chen SL, Himo F, Almo SC, Raushel FM
Biochemistry 47 9497-504 (2008)
PMID: 18702530

Function and Biology Details

Reaction catalysed: 
An aryl dialkyl phosphate + H(2)O = dialkyl phosphate + an aryl alcohol
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141251 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Parathion hydrolase Chains: A, B
Molecule details ›
Chains: A, B
Length: 331 amino acids
Theoretical weight: 35.96 KDa
Source organism: Brevundimonas diminuta
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A434 (Residues: 35-365; Coverage: 99%)
Gene name: opd
Sequence domains: Phosphotriesterase family
Structure domains: Metal-dependent hydrolases

Ligands and Environments

4 bound ligands:
Ligand CO 4 x CO
Ligand BTB 2 x BTB
Ligand DPF 1 x DPF
Ligand EFS 1 x EFS
1 modified residue:
Ligand KCX 2 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P1
Unit cell:
a: 43.286Å b: 45.338Å c: 78.913Å
α: 104.73° β: 93.4° γ: 97.65°
R-values:
R R work R free
0.143 0.14 0.196
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies.
Kamerlin et al. (2009)
4 more

3 mentions without citation

Organophosphorus Nerve Agents: Types, Toxicity, and Treatments.
Mukherjee et al. (2020)
2 more