3EY0

A new form of DNA-drug interaction in the minor groove of a coiled coil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Coiled-coil conformation of a pentamidine-DNA complex

Moreno, T.Pous, J.Subirana, J.A.Campos, J.L.

(2010) Acta Crystallogr.,Sect.D 66: 251-257

  • DOI: 10.1107/S0907444909055693

  • PubMed Abstract: 
  • The coiled-coil structure formed by the complex of the DNA duplex d(ATATATATAT)(2) with pentamidine is presented. The duplex was found to have a mixed structure containing Watson-Crick and Hoogsteen base pairs. The drug stabilizes the coiled coil thr ...

    The coiled-coil structure formed by the complex of the DNA duplex d(ATATATATAT)(2) with pentamidine is presented. The duplex was found to have a mixed structure containing Watson-Crick and Hoogsteen base pairs. The drug stabilizes the coiled coil through the formation of cross-links between neighbouring duplexes. The central part of the drug is found in the minor groove as expected, whereas the charged terminal amidine groups protrude and interact with phosphates from neighbouring molecules. The formation of cross-links may be related to the biological effects of pentamidine, which is used as an antiprotozoal agent in trypanosomiasis, leishmaniasis and pneumonias associated with AIDS. The DNA sequence that was used is highly abundant in most eukaryotic genomes. However, very few data are available on DNA sequences which only contain A.T base pairs.


    Organizational Affiliation

    Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, E-08028 Barcelona, Spain.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DAP*DTP*DAP*DT)-3'A,B10N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNT
Query on PNT

Download SDF File 
Download CCD File 
A
1,5-BIS(4-AMIDINOPHENOXY)PENTANE
C19 H24 N4 O2
XDRYMKDFEDOLFX-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.216 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 27.789α = 90.00
b = 27.789β = 90.00
c = 311.950γ = 120.00
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance