› 5jf3

X-ray diffraction
1.6Å resolution

Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor AT018

Released:
DOI: 10.2210/pdb5jf3/pdb
PDB entry 5jf3 coloured by chain, front view.
PDB entry 5jf3 coloured by chain, side view.
PDB entry 5jf3 coloured by chain, top view.
Source organism: Streptococcus agalactiae
Primary publication:
A unique peptide deformylase platform to rationally design and challenge novel active compounds.
Fieulaine S, Alves de Sousa R, Maigre L, Hamiche K, Alimi M, Bolla JM, Taleb A, Denis A, Pagès JM, Artaud I, Meinnel T, Giglione C
Sci Rep 6 35429 (2016)
PMID: 27762275

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-184298 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase Chain: A
Molecule details ›
Chain: A
Length: 204 amino acids
Theoretical weight: 22.89 KDa
Source organism: Streptococcus agalactiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8E378 (Residues: 1-204; Coverage: 100%)
Gene names: def, gbs1883
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

4 bound ligands:
Ligand SF5 1 x SF5
Ligand ACT 1 x ACT
Ligand IMD 1 x IMD
Ligand ZN 9 x ZN
1 modified residue:
Ligand OCS 1 x OCS

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P212121
Unit cell:
a: 41.07Å b: 65.49Å c: 88.79Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.186 0.214
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Metal utilization in genome-reduced bacteria: Do human mycoplasmas rely on iron?
Perálvarez-Marín et al. (2021)
5 other articles