3DPO

Crystal structure of the substrate binding domain of E. coli DnaK in complex with a short pyrrhocoricin-derived inhibitor peptide

Structural Biology Knowledgebase: 3DPO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.178

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3DPO

Classification: Chaperone Peptide Binding Protein

Total Structure Weight: 50931.69

Macromolecule Entities
Molecule Chains Length Organism Details
Chaperone protein dnaK A, B 219 Escherichia coli Fragment: Substrate binding domain (UNP residues 389 to 607)
Gene Name(s): dnaK groP grpF seg b0014 JW0013
inhibitor peptide C, D 11 Pyrrhocoris apterus Gene Name(s):

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
ALC
Query on ALC
C, D L-PEPTIDE LINKING C9 H17 N O2 ALA

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.178
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 77.58 α = 90.00
b = 159.96 β = 90.00
c = 44.93 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-07-09
  • Released Date: 2009-03-10
  • Deposition author(s): Roujeinikova, A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4