4XE2 | pdb_00004xe2

N-terminal domain of Hsp90 from Dictyostelium discoideum in complex with peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4XE2

This is version 1.2 of the entry. See complete history

Literature

First Structural View of a Peptide Interacting with the Nucleotide Binding Domain of Heat Shock Protein 90.

Raman, S.Singh, M.Tatu, U.Suguna, K.

(2015) Sci Rep 5: 17015-17015

  • DOI: https://doi.org/10.1038/srep17015
  • Primary Citation Related Structures: 
    4XC0, 4XCJ, 4XCL, 4XD8, 4XDM, 4XE2, 4XKA, 4XKO

  • PubMed Abstract: 

    The involvement of Hsp90 in progression of diseases like cancer, neurological disorders and several pathogen related conditions is well established. Hsp90, therefore, has emerged as an attractive drug target for many of these diseases. Several small molecule inhibitors of Hsp90, such as geldanamycin derivatives, that display antitumor activity, have been developed and are under clinical trials. However, none of these tested inhibitors or drugs are peptide-based compounds. Here we report the first crystal structure of a peptide bound at the ATP binding site of the N-terminal domain of Hsp90. The peptide makes several specific interactions with the binding site residues, which are comparable to those made by the nucleotide and geldanamycin. A modified peptide was designed based on these interactions. Inhibition of ATPase activity of Hsp90 was observed in the presence of the modified peptide. This study provides an alternative approach and a lead peptide molecule for the rational design of effective inhibitors of Hsp90 function.


  • Organizational Affiliation
    • Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

Macromolecule Content 

  • Total Structure Weight: 29.23 kDa 
  • Atom Count: 2,115 
  • Modeled Residue Count: 221 
  • Deposited Residue Count: 259 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heat shock cognate 90 kDa protein259Dictyostelium discoideumMutation(s): 0 
Gene Names: hspDhsc90hsp90DDB_G0267400
UniProt
Find proteins for P54651 (Dictyostelium discoideum)
Explore P54651 
Go to UniProtKB:  P54651
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54651
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.913α = 90
b = 46.63β = 107.12
c = 59.787γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-02
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description