Crystal structure of helicobacter pylori ClpX

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.219 

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Crystal Structure of ClpX Molecular Chaperone from Helicobacter pylori

Kim, D.Y.Kim, K.K.

(2003) J Biol Chem 278: 50664-50670

  • DOI: https://doi.org/10.1074/jbc.M305882200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    ClpX, a heat shock protein 100 chaperone, which acts as the regulatory subunit of the ATP-dependent ClpXP protease, is responsible for intracellular protein remodeling and degradation. To provide a structural basis for a better understanding of the function of the Clp ATPase family, the crystal structures of Helicobacter pylori ClpX, lacking an N-terminal Cys cluster region complexed with ADP, was determined. The overall structure of ClpX is similar to that of heat shock locus U (HslU), consisting of two subdomains, with ADP bound at the subdomain interface. The crystal structure of ClpX reveals that a conserved tripeptide (LGF) is located on the tip of ClpP binding loop extending from the N-terminal subdomain. A hexameric model of ClpX suggests that six tripeptides make hydrophobic contacts with the hydrophobic clefts of the ClpP heptmer asymmetrically. In addition, the nucleotide binding environment provides the structural explanation for the hexameric assembly and the modulation of ATPase activity.

  • Organizational Affiliation

    Department of Molecular Cell Biology, Center for Molecular Medicine, SBRI, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease ATP-binding subunit clpX376Helicobacter pylori 26695Mutation(s): 0 
Gene Names: CLPX
Find proteins for O25926 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25926 
Go to UniProtKB:  O25926
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25926
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
C10 H15 N5 O10 P2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.219 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.515α = 90
b = 78.515β = 90
c = 131.514γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations