› 3str

X-ray diffraction
1.75Å resolution

Strep Peptide Deformylase with a time dependent thiazolidine hydroxamic acid

Released:
DOI: 10.2210/pdb3str/pdb
PDB entry 3str coloured by chain, front view.
PDB entry 3str coloured by chain, side view.
PDB entry 3str coloured by chain, top view.
Source organism: Streptococcus pneumoniae
Primary publication:
Understanding the origins of time-dependent inhibition by polypeptide deformylase inhibitors.
Totoritis R, Duraiswami C, Taylor AN, Kerrigan JJ, Campobasso N, Smith KJ, Ward P, King BW, Murrayz-Thompson M, Jones AD, Van Aller GS, Aubart KM, Zalacain M, Thrall SH, Meek TD, Schwartz B
Biochemistry 50 6642-54 (2011)
PMID: 21711014

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-188029 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase Chain: P
Molecule details ›
Chain: P
Length: 203 amino acids
Theoretical weight: 22.72 KDa
Source organism: Streptococcus pneumoniae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q939R9 (Residues: 1-203; Coverage: 100%)
Gene names: A5N45_09745, AZJ70_00135, GM535_00135, GM536_05180, GM537_01960, GM545_05305, SAMEA3381574_00169, SAMEA3431391_01242, def, defB, def_1, def_2
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

4 bound ligands:
Ligand NI 1 x NI
Ligand SO4 4 x SO4
Ligand 3LI 1 x 3LI
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P43
Unit cell:
a: 50.274Å b: 50.274Å c: 91.486Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.192 0.23
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

Frequency of Spontaneous Resistance to Peptide Deformylase Inhibitor GSK1322322 in Haemophilus influenzae, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae.
Min et al. (2015)
1 more

2 mentions without citation

Fixed-parameter tractable sampling for RNA design with multiple target structures.
Hammer et al. (2019)
1 more