1A2E

CRYSTAL STRUCTURE OF A DOUBLE-STRANDED DNA DECAMER CONTAINING A CISPLATIN INTERSTRAND CROSS-LINK ADDUCT

  • Classification: DNA

  • Deposited: 1998-01-05 Released: 1999-04-12 
  • Deposition Author(s): Coste, F., Zelwer, C.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a double-stranded DNA containing a cisplatin interstrand cross-link at 1.63 A resolution: hydration at the platinated site.

Coste, F.Malinge, J.M.Serre, L.Shepard, W.Roth, M.Leng, M.Zelwer, C.

(1999) Nucleic Acids Res. 27: 1837-1846


  • PubMed Abstract: 
  • cis-diamminedichloroplatinum (II) (cisplatin) is a powerful anti-tumor drug whose target is cellular DNA. In the reaction between DNA and cisplatin, covalent intrastrand and interstrand cross-links (ICL) are formed. Two solution structures of the ICL ...

    cis-diamminedichloroplatinum (II) (cisplatin) is a powerful anti-tumor drug whose target is cellular DNA. In the reaction between DNA and cisplatin, covalent intrastrand and interstrand cross-links (ICL) are formed. Two solution structures of the ICL have been published recently. In both models the double-helix is bent and unwound but with significantly different angle values. We solved the crystal structure at 100K of a double-stranded DNA decamer containing a single cisplatin ICL, using the anomalous scattering (MAD) of platinum as a unique source of phase information. We found 47 degrees for double-helix bending and 70 degrees for unwinding in agreement with previous electrophoretic assays. The crystals are stabilized by intermolecular contacts involving two cytosines extruded from the double-helix, one of which makes a triplet with a terminal G.C pair. The platinum coordination is nearly square and the platinum residue is embedded into a cage of nine water molecules linked to the cross-linked guanines, to the two amine groups, and to the phosphodiester backbone through other water molecules. This water molecule organization is discussed in relation with the chemical stability of the ICL.


    Organizational Affiliation

    Centre de Biophysique Moléculaire, Centre de National de la Recherche Scientifique, affiliated to the Université d'Orléans, rue Charles Sadron, 45071 Orleans Cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*TP*CP*GP*CP*TP*CP*TP*C)-3')A10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*GP*AP*GP*CP*GP*AP*GP*G)-3')B10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPT
Query on CPT

Download SDF File 
Download CCD File 
A
Cisplatin
diammine(dichloro)platinum
Cl2 H6 N2 Pt
LXZZYRPGZAFOLE-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 42.890α = 90.00
b = 29.980β = 95.98
c = 46.570γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SHARPphasing
CCP4data scaling
SHELXL-96refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1998-01-05 
  • Released Date: 1999-04-12 
  • Deposition Author(s): Coste, F., Zelwer, C.

Revision History 

  • Version 1.0: 1999-04-12
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance