› 2ew6

X-ray diffraction
2.2Å resolution

Structure of Helicobacter Pylori peptide deformylase in complex with inhibitor

Released:
DOI: 10.2210/pdb2ew6/pdb
PDB entry 2ew6 coloured by chain, front view.
PDB entry 2ew6 coloured by chain, side view.
PDB entry 2ew6 coloured by chain, top view.
Source organism: Helicobacter pylori
Primary publication:
Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: reverse docking, enzymatic assay, and X-ray crystallography validation.
Cai J, Han C, Hu T, Zhang J, Wu D, Wang F, Liu Y, Ding J, Chen K, Yue J, Shen X, Jiang H
Protein Sci 15 2071-81 (2006)
PMID: 16882991

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-179288 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase Chain: A
Molecule details ›
Chain: A
Length: 181 amino acids
Theoretical weight: 21.01 KDa
Source organism: Helicobacter pylori
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q672W7 (Residues: 2-174; Coverage: 99%)
Gene name: def
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

2 bound ligands:
Ligand CO 1 x CO
Ligand Y13 1 x Y13
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P212121
Unit cell:
a: 42.17Å b: 52.937Å c: 91.792Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.204 0.243
Expression system: Escherichia coli BL21(DE3)

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Citations

19 review citations

The value of natural products to future pharmaceutical discovery.
Baker et al. (2007)
18 more

1 mention 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)