› 3g6n

X-ray diffraction
2.5Å resolution

Crystal structure of an EfPDF complex with Met-Ala-Ser

Released:
DOI: 10.2210/pdb3g6n/pdb
PDB entry 3g6n coloured by chain, front view.
PDB entry 3g6n coloured by chain, side view.
PDB entry 3g6n coloured by chain, top view.
Source organism: Enterococcus faecium
Primary publication:
Crystal structure of an EfPDF complex with Met-Ala-Ser based on crystallographic packing.
Nam KH, Kim KH, Kim EE, Hwang KY
Biochem Biophys Res Commun 381 630-3 (2009)
PMID: 19249287

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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-163581 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Peptide deformylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 191 amino acids
Theoretical weight: 21.25 KDa
Source organism: Enterococcus faecium
Expression system: Escherichia coli
UniProt:
  • Canonical: Q842S4 (Residues: 1-187; Coverage: 100%)
Gene names: AWT83_02740, B1P95_00480, B4W81_03530, CQR37_04965, CUN04_02265, EB12_01528, FIU59_02130, GBM44_00970, GBM73_08910, M3X98_00055, def
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase
peptide (Met)(Ala)(Ser) Chains: F, G
Molecule details ›
Chains: F, G
Length: 3 amino acids
Theoretical weight: 307 Da
Source organism: Enterococcus faecium
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand FE 2 x FE
Ligand NA 5 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 4A
Spacegroup: P6422
Unit cell:
a: 148.688Å b: 148.688Å c: 141.902Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.225 0.225 0.247
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 citation in other articles

VitAL: Viterbi algorithm for de novo peptide design.
Unal et al. (2010)
2 more