› 2okl

X-ray diffraction
1.7Å resolution

Crystal structure of Peptide Deformylase 2 with actinonin from Bacillus cereus

Released:
DOI: 10.2210/pdb2okl/pdb
PDB entry 2okl coloured by chain, front view.
PDB entry 2okl coloured by chain, side view.
PDB entry 2okl coloured by chain, top view.
Source organism: Bacillus cereus ATCC 14579
Primary publication:
Characterization of peptide deformylase2 from B. cereus.
Park JK, Kim KH, Moon JH, Kim EE
J Biochem Mol Biol 40 1050-7 (2007)
PMID: 18047803

Function and Biology Details

Reaction catalysed: 
Formyl-L-methionyl peptide + H(2)O = formate + methionyl peptide
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-182457 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 185 amino acids
Theoretical weight: 20.64 KDa
Source organism: Bacillus cereus ATCC 14579
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q819K2 (Residues: 1-184; Coverage: 100%)
Gene names: BC_3974, def2
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand BB2 4 x BB2
Ligand CIT 1 x CIT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 4A, PAL/PLS BEAMLINE 6B
Spacegroup: P6522
Unit cell:
a: 69.447Å b: 69.447Å c: 294.412Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.228 0.228 0.257
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Peptide deformylase--a promising therapeutic target for tuberculosis and antibacterial drug discovery.
Sharma et al. (2009)

1 mention without citation

The Search for Herbal Antibiotics: An In-Silico Investigation of Antibacterial Phytochemicals.
Snow Setzer et al. (2016)