› 3qnj

X-ray diffraction
2.28Å resolution

Crystal structure of the substrate binding domain of E.coli DnaK in complex with the antimicrobial peptide oncocin

Released:
DOI: 10.2210/pdb3qnj/pdb
PDB entry 3qnj coloured by chain, front view.
PDB entry 3qnj coloured by chain, side view.
PDB entry 3qnj coloured by chain, top view.
Source organisms:
Primary publication:
Rational design of oncocin derivatives with superior protease stabilities and antibacterial activities based on the high-resolution structure of the oncocin-DnaK complex.
Knappe D, Zahn M, Sauer U, Schiffer G, Sträter N, Hoffmann R
Chembiochem 12 874-6 (2011)
PMID: 21387510

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-141455 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Chaperone protein DnaK Chains: A, B
Molecule details ›
Chains: A, B
Length: 219 amino acids
Theoretical weight: 23.82 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A6Y8 (Residues: 389-607; Coverage: 34%)
Gene names: JW0013, b0014, dnaK, groP, grpF, seg
Sequence domains: Hsp70 protein
Structure domains:
antimicrobial peptide oncocin Chains: C, D
Molecule details ›
Chains: C, D
Length: 19 amino acids
Theoretical weight: 2.31 KDa
Source organism: Oncopeltus fasciatus
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand SO4 6 x SO4
1 modified residue:
Ligand ORN 4 x ORN

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.3
Spacegroup: P21212
Unit cell:
a: 77.664Å b: 161.137Å c: 44.629Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.211 0.284
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

8 review citations

Intracellular Targeting Mechanisms by Antimicrobial Peptides.
Le et al. (2017)
7 more

1 mention without citation

DnaK as Antibiotic Target: Hot Spot Residues Analysis for Differential Inhibition of the Bacterial Protein in Comparison with the Human HSP70.
Chiappori et al. (2015)