4JWE

Crystal structure of the substrate binding domain of E.coli DnaK in complex with sheep Bac7(1-21)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Identification of DnaK Binding Sites within Bovine and Sheep Bactenecin Bac7.

Zahn, M.Kieslich, B.Berthold, N.Knappe, D.Hoffmann, R.Strater, N.

(2014) Protein Pept.Lett. 21: 407-412

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial resistance against common antibiotics is an increasing health problem. New pharmaceuticals for the treatment of infections caused by resistant pathogens are needed. Small proline-rich antimicrobial peptides (PrAMPs) from insects are known t ...

    Bacterial resistance against common antibiotics is an increasing health problem. New pharmaceuticals for the treatment of infections caused by resistant pathogens are needed. Small proline-rich antimicrobial peptides (PrAMPs) from insects are known to bind intracellularly to the conventional substrate binding cleft of the E. coli Hsp70 chaperone DnaK. Furthermore, bactenecins from mammals, members of the cathelicidin family, also contain potential DnaK binding sites. Crystal structures of bovine and sheep Bac7 in complex with the DnaK substrate binding domain show that the peptides bind in the forward binding mode with a leucine positioned in the central hydrophobic pocket. In most structures, proline and arginine residues preceding leucine occupy the hydrophobic DnaK binding sites -1 and -2. Within bovine Bac7, four potential DnaK binding sites were identified.


    Organizational Affiliation

    Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany. strater@bbz.uni-leipzig.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chaperone protein DnaK
A, B
219Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dnaK (groP, grpF, seg)
Find proteins for P0A6Y8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6Y8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cathelicidin-3
C, D
21Ovis ariesMutation(s): 0 
Gene Names: CATHL3 (BAC7, BAC7.5)
Find proteins for P50415 (Ovis aries)
Go to UniProtKB:  P50415
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.659α = 90.00
b = 162.531β = 90.00
c = 44.783γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
MAR345data collection
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-03-27 
  • Released Date: 2013-11-13 
  • Deposition Author(s): Zahn, M., Straeter, N.

Revision History 

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2014-03-26
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description