3CGY

Crystal Structure of Salmonella Sensor Kinase PhoQ catalytic domain in complex with radicicol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.246 

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This is version 1.2 of the entry. See complete history


Literature

The Hsp90 inhibitor radicicol interacts with the ATP-binding pocket of bacterial sensor kinase PhoQ.

Guarnieri, M.T.Zhang, L.Shen, J.Zhao, R.

(2008) J Mol Biol 379: 82-93

  • DOI: https://doi.org/10.1016/j.jmb.2008.03.036
  • Primary Citation of Related Structures:  
    3CGY, 3CGZ

  • PubMed Abstract: 

    Sensor kinases in the bacterial two-component system share a unique ATP-binding Bergerat fold with the GHL (gyrase, Hsp90, and MutL) family of proteins. We demonstrated that selected GHL inhibitors bind to the catalytic domain of sensor kinase PhoQ (PhoQcat) using NMR chemical shift perturbation experiments. Using crystallographic approaches, we show that radicicol (an Hsp90 inhibitor) binds and interacts specifically with residues in the ATP-binding pocket of PhoQ. The interaction between radicicol and PhoQcat demonstrates significant similarities as well as differences compared to AMPPNP (a non-hydrolyzable ATP analog) bound to PhoQcat and radicicol bound to Hsp90. Our results suggest that GHL inhibitors may be useful lead compounds for developing sensor kinase inhibitors.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Virulence sensor histidine kinase phoQ
A, B, C
157Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: phoQ
EC: 2.7.13.3
UniProt
Find proteins for P0DM80 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P0DM80 
Go to UniProtKB:  P0DM80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DM80
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
RDC BindingDB:  3CGY Kd: 7.15e+5 (nM) from 1 assay(s)
PDBBind:  3CGY Kd: 7.15e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.246 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.923α = 90
b = 63.759β = 121.41
c = 87.772γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description