› 3g5p

X-ray diffraction
1.7Å resolution

Structure and activity of human mitochondrial peptide deformylase, a novel cancer target

Released:
DOI: 10.2210/pdb3g5p/pdb
PDB entry 3g5p coloured by chain, front view.
PDB entry 3g5p coloured by chain, side view.
PDB entry 3g5p coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure and activity of human mitochondrial peptide deformylase, a novel cancer target.
Escobar-Alvarez S, Goldgur Y, Yang G, Ouerfelli O, Li Y, Scheinberg DA
J Mol Biol 387 1211-28 (2009)
PMID: 19236878

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
homo tetramer
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190753 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase, mitochondrial Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 183 amino acids
Theoretical weight: 20.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9HBH1 (Residues: 64-243; Coverage: 74%)
Gene names: PDF, PDF1A
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

2 bound ligands:
Ligand CO 4 x CO
Ligand PO4 8 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: C2
Unit cell:
a: 116.332Å b: 77.825Å c: 111.041Å
α: 90° β: 107.93° γ: 90°
R-values:
R R work R free
0.162 0.161 0.187
Expression system: Escherichia coli

Quick links

Citations

5 review citations

The role of formylated peptides and formyl peptide receptor 1 in governing neutrophil function during acute inflammation.
Dorward et al. (2015)
4 more

3 mentions without citation

High-resolution analysis and functional mapping of cleavage sites and substrate proteins of furin in the human proteome.
Shiryaev et al. (2013)
2 more