Crystal structure of cisplatin bound to a human copper chaperone (monomer) - new refinement

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 

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Ligand Structure Quality Assessment 

This is version 1.7 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3iwl


Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin.

Shabalin, I.Dauter, Z.Jaskolski, M.Minor, W.Wlodawer, A.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1965-1979

  • DOI: https://doi.org/10.1107/S139900471500629X
  • Primary Citation of Related Structures:  
    4YDX, 4YEA, 4YEM, 4YEN, 4YEO

  • PubMed Abstract: 

    The anticancer activity of platinum-containing drugs such as cisplatin and carboplatin is considered to primarily arise from their interactions with nucleic acids; nevertheless, these drugs, or the products of their hydrolysis, also bind to proteins, potentially leading to the known side effects of the treatments. Here, over 40 crystal structures deposited in the Protein Data Bank (PDB) of cisplatin and carboplatin complexes of several proteins were analysed. Significant problems of either a crystallographic or a chemical nature were found in most of the presented atomic models and they could be traced to less or more serious deficiencies in the data-collection and refinement procedures. The re-evaluation of these data and models was possible thanks to their mandatory or voluntary deposition in publicly available databases, emphasizing the point that the availability of such data is critical for making structural science reproducible. Based on this analysis of a selected group of macromolecular structures, the importance of deposition of raw diffraction data is stressed and a procedure for depositing, tracking and using re-refined crystallographic models is suggested.

  • Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Copper transport protein ATOX167Homo sapiensMutation(s): 0 
Gene Names: ATOX1HAH1
UniProt & NIH Common Fund Data Resources
Find proteins for O00244 (Homo sapiens)
Explore O00244 
Go to UniProtKB:  O00244
PHAROS:  O00244
GTEx:  ENSG00000177556 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00244
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.07α = 90
b = 54.07β = 90
c = 55.578γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
Cootmodel building
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-07-08
    Changes: Database references
  • Version 1.2: 2015-09-09
    Changes: Database references
  • Version 1.3: 2015-09-16
    Changes: Database references
  • Version 1.4: 2017-09-06
    Changes: Author supporting evidence, Derived calculations
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence, Derived calculations
  • Version 1.6: 2022-04-13
    Changes: Database references, Structure summary
  • Version 1.7: 2023-09-27
    Changes: Data collection, Refinement description