1Z3F

Structure of ellipticine in complex with a 6-bp DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The anticancer agent ellipticine unwinds DNA by intercalative binding in an orientation parallel to base pairs.

Canals, A.Purciolas, M.Aymami, J.Coll, M.

(2005) Acta Crystallogr.,Sect.D 61: 1009-1012

  • DOI: 10.1107/S0907444905015404

  • PubMed Abstract: 
  • Ellipticine is a natural plant product that has been found to be a powerful anticancer drug. Although still unclear, its mechanism of action is considered to be mainly based on DNA intercalation and/or the inhibition of topoisomerase II. Many experim ...

    Ellipticine is a natural plant product that has been found to be a powerful anticancer drug. Although still unclear, its mechanism of action is considered to be mainly based on DNA intercalation and/or the inhibition of topoisomerase II. Many experimental data suggest an intercalation based on stacking interactions along the major base-pair axis, but alternative binding modes have been proposed, in particular for ellipticine derivatives. The 1.5 A resolution structure of ellipticine complexed to a 6 bp oligonucleotide unveils its mode of binding and enables a detailed analysis of the distorting effects of the drug on the DNA.


    Organizational Affiliation

    Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain. acpcri@ibmb.csic.es




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*GP*AP*TP*CP*G)-3'A,B6N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EL
Query on EL

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Download CCD File 
A, B
ELLIPTICINE
C17 H15 N2
CTSPAMFJBXKSOY-UHFFFAOYSA-O
 Ligand Interaction
CO
Query on CO

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Download CCD File 
A, B
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.220 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 24.860α = 90.00
b = 24.860β = 90.00
c = 78.860γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
AMoREphasing
ProDCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description