› 3dpq

X-ray diffraction
2.6Å resolution

Crystal structure of the substrate binding domain of E. coli DnaK in complex with a long pyrrhocoricin-derived inhibitor peptide (form B)

Released:
DOI: 10.2210/pdb3dpq/pdb
PDB entry 3dpq coloured by chain, front view.
PDB entry 3dpq coloured by chain, side view.
PDB entry 3dpq coloured by chain, top view.
Source organisms:
Primary publication:
Allosteric coupling between the lid and interdomain linker in DnaK revealed by inhibitor binding studies.
Liebscher M, Roujeinikova A
J Bacteriol 191 1456-62 (2009)
PMID: 19103929

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141449 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Chaperone protein DnaK Chains: A, B, E, F
Molecule details ›
Chains: A, B, E, F
Length: 219 amino acids
Theoretical weight: 23.82 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A6Y8 (Residues: 389-607; Coverage: 34%)
Gene names: JW0013, b0014, dnaK, groP, grpF, seg
Sequence domains: Hsp70 protein
Structure domains:
Pyrrhocoricin Chains: C, D, G, H
Molecule details ›
Chains: C, D, G, H
Length: 20 amino acids
Theoretical weight: 2.47 KDa
Source organism: Pyrrhocoris apterus
Expression system: Not provided
UniProt:
  • Canonical: P37362 (Residues: 1-20; Coverage: 100%)

Ligands and Environments

1 bound ligand:
Ligand SO4 1 x SO4
1 modified residue:
Ligand ALC 4 x ALC

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P212121
Unit cell:
a: 77.712Å b: 91.653Å c: 154.797Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.257 0.254 0.319
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

Proline-rich antimicrobial peptides: converging to a non-lytic mechanism of action.
Scocchi et al. (2011)
3 more

3 mentions without citation

A History of Molecular Chaperone Structures in the Protein Data Bank.
Bascos et al. (2019)
2 more