198D

A TRIGONAL FORM OF THE IDARUBICIN-D(CGATCG) COMPLEX: CRYSTAL AND MOLECULAR STRUCTURE AT 2.0 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A trigonal form of the idarubicin:d(CGATCG) complex; crystal and molecular structure at 2.0 A resolution.

Dautant, A.Langlois d'Estaintot, B.Gallois, B.Brown, T.Hunter, W.N.

(1995) Nucleic Acids Res. 23: 1710-1716


  • PubMed Abstract: 
  • The X-ray crystal structure of the complex between the anthracycline idarubicin and d(CGATCG) has been solved by molecular replacement and refined to a resolution of 2.0 A. The final R-factor is 0.19 for 3768 reflections with Fo > or = 2 sigma (Fo). ...

    The X-ray crystal structure of the complex between the anthracycline idarubicin and d(CGATCG) has been solved by molecular replacement and refined to a resolution of 2.0 A. The final R-factor is 0.19 for 3768 reflections with Fo > or = 2 sigma (Fo). The complex crystallizes in the trigonal space group P31 with unit cell parameters a = b = 52.996(4), c = 33.065(2) A, alpha = beta = 90 degree, gamma = 120 degree. The asymmetric unit consists of two duplexes, each one being complexed with two idarubicin drugs intercalated at the CpG steps, one spermine and 160 water molecules. The molecular packing underlines major groove-major groove interactions between neighbouring helices, and an unusually low value of the occupied fraction of the unit cell due to a large solvent channel of approximately 30 A diameter. This is the first trigonal crystal form of a DNA-anthracycline complex. The structure is compared with the previously reported structure of the same complex crystallizing in a tetragonal form. The geometry of both the double helices and the intercalation site are conserved as are the intramolecular interactions despite the different crystal forms.


    Related Citations: 
    • Influence of Aglycone Modifications on the Binding of Anthracycline Drugs to DNA: The Molecular Structure of Idarubicin and 4-O-Demethyl-11-Deoxydoxorubicin Complexed to d(CGATCG)
      Gao, Y.-G.,Wang, A.H.-J.
      (1991) Anti-Cancer Drug Des. 6: 137


    Organizational Affiliation

    Laboratoire de Cristallographie, ERS CNRS 133, Université de Bordeaux I, Talence, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')A,B,C,D6N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

Download SDF File 
Download CCD File 
A
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
DM5
Query on DM5

Download SDF File 
Download CCD File 
A, B, D
IDARUBICIN
4-DEMETHOXY-DAUNORUBICIN
C26 H27 N O9
XDXDZDZNSLXDNA-TZNDIEGXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 52.996α = 90.00
b = 52.996β = 90.00
c = 33.065γ = 120.00
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-03-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance