› 4e81

X-ray diffraction
1.9Å resolution

Crystal structure of the substrate binding domain of E.coli DnaK in complex with a short apidaecin peptide

Released:
DOI: 10.2210/pdb4e81/pdb
PDB entry 4e81 coloured by chain, front view.
PDB entry 4e81 coloured by chain, side view.
PDB entry 4e81 coloured by chain, top view.
Source organisms:
Primary publication:
Api88 is a novel antibacterial designer peptide to treat systemic infections with multidrug-resistant Gram-negative pathogens.
Czihal P, Knappe D, Fritsche S, Zahn M, Berthold N, Piantavigna S, Müller U, Van Dorpe S, Herth N, Binas A, Köhler G, De Spiegeleer B, Martin LL, Nolte O, Sträter N, Alber G, Hoffmann R
ACS Chem Biol 7 1281-91 (2012)
PMID: 22594381

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141462 (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:
Apidaecin-1A Chains: C, D
Molecule details ›
Chains: C, D
Length: 10 amino acids
Theoretical weight: 1.21 KDa
Source organism: Apis mellifera
Expression system: Not provided
UniProt:
  • Canonical: Q06602 (Residues: 268-279; Coverage: 4%)
Gene name: APID73
Sequence domains: Apidaecin

Ligands and Environments

1 bound ligand:
Ligand SO4 3 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P21212
Unit cell:
a: 144.777Å b: 60.202Å c: 67.453Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.208 0.259
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

11 review citations

How hsp70 molecular machines interact with their substrates to mediate diverse physiological functions.
Clerico et al. (2015)
10 more

3 mentions without citation

An atomistic view of Hsp70 allosteric crosstalk: from the nucleotide to the substrate binding domain and back.
Chiappori et al. (2016)
2 more