4YDX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history

Re-refinement Note

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


Literature

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: 10.1107/S139900471500629X
  • Primary Citation of Related Structures:  
    4YDX, 4YEM, 4YEN, 4YEO, 4YEA

  • 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 ...

    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.


    Related Citations: 
    • Crystal structures of cisplatin bound to a human copper chaperone.
      Boal, A.K., Rosenzweig, A.C.
      (2009) J Am Chem Soc 131: 14196

    Organizational Affiliation

    Protein Structure Section, MCL, National Cancer Institute, Frederick, MD 21702, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Copper transport protein ATOX1A67Homo sapiensMutation(s): 0 
Gene Names: ATOX1HAH1
Find proteins for O00244 (Homo sapiens)
Explore O00244 
Go to UniProtKB:  O00244
NIH Common Fund Data Resources
PHAROS:  O00244
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TCE
Query on TCE

Download Ideal Coordinates CCD File 
D [auth A]3,3',3''-phosphanetriyltripropanoic acid
C9 H15 O6 P
PZBFGYYEXUXCOF-UHFFFAOYSA-N
 Ligand Interaction
PT
Query on PT

Download Ideal Coordinates CCD File 
B [auth A]PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
SHARPphasing
Cootmodel building
HKL-2000data scaling

Structure Validation

View Full Validation Report



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