› 3u7k

X-ray diffraction
1.9Å resolution

Crystal structures of the Staphylococcus aureus peptide deformylase in complex with two classes of new inhibitors

Released:
DOI: 10.2210/pdb3u7k/pdb
PDB entry 3u7k coloured by chain, front view.
PDB entry 3u7k coloured by chain, side view.
PDB entry 3u7k coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus COL
Primary publication:
Structures of Staphylococcus aureus peptide deformylase in complex with two classes of new inhibitors.
Lee SJ, Lee SJ, Lee SK, Yoon HJ, Lee HH, Kim KK, Lee BJ, Lee BI, Suh SW
Acta Crystallogr D Biol Crystallogr 68 784-93 (2012)
PMID: 22751663

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-177198 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase Chain: A
Molecule details ›
Chain: A
Length: 191 amino acids
Theoretical weight: 21.69 KDa
Source organism: Staphylococcus aureus subsp. aureus COL
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5HGZ3 (Residues: 1-183; Coverage: 100%)
Gene names: SACOL1100, def, def1, pdf1
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

2 bound ligands:
Ligand MDB 1 x MDB
Ligand ZN 1 x ZN
1 modified residue:
Ligand CSD 1 x CSD

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: C2221
Unit cell:
a: 93.776Å b: 120.269Å c: 47.753Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.214 0.266
Expression system: Escherichia coli

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Citations

3 citation in other articles

Discovery of Potential Plant-Derived Peptide Deformylase (PDF) Inhibitors for Multidrug-Resistant Bacteria Using Computational Studies.
Rampogu et al. (2018)
2 more

1 mention without citation

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