› 1ix1

X-ray diffraction
1.85Å resolution

Crystal Structure of P.aeruginosa Peptide deformylase Complexed with Antibiotic Actinonin

Released:
DOI: 10.2210/pdb1ix1/pdb
PDB entry 1ix1 coloured by chain, front view.
PDB entry 1ix1 coloured by chain, side view.
PDB entry 1ix1 coloured by chain, top view.
Source organism: Pseudomonas aeruginosa
Primary publication:
Crystal structure of peptide deformylase from Staphylococcus aureus in complex with actinonin, a naturally occurring antibacterial agent.
Yoon HJ, Kim HL, Lee SK, Kim HW, Kim HW, Lee JY, Mikami B, Suh SW
Proteins 57 639-42 (2004)
PMID: 15382235

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 domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-191503 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 171 amino acids
Theoretical weight: 19.81 KDa
Source organism: Pseudomonas aeruginosa
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9I7A8 (Residues: 1-168; Coverage: 100%)
Gene names: PA0019, def
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand BB2 2 x BB2
Ligand MHA 2 x MHA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 6B
Spacegroup: P212121
Unit cell:
a: 68.75Å b: 74.46Å c: 77.18Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.185 0.214
Expression system: Escherichia coli

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Citations

11 citation in other articles

Validation of Putative Apicoplast-Targeting Drugs Using a Chemical Supplementation Assay in Cultured Human Malaria Parasites.
Uddin et al. (2018)
10 more

5 mentions without citation

Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: reverse docking, enzymatic assay, and X-ray crystallography validation.
Cai et al. (2006)
4 more