3EY0 image
Deposition Date 2008-10-17
Release Date 2009-10-27
Last Version Date 2024-04-03
Entry Detail
PDB ID:
3EY0
Keywords:
DNA
Title:
A new form of DNA-drug interaction in the minor groove of a coiled coil
Biological Source:
Source Organism:
(Taxon ID: )
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.52 Å
R-Value Free:
0.27
R-Value Work:
0.21
R-Value Observed:
0.22
Space Group:
P 65 2 2
3EY0 validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DAP*DTP*DAP*DT)-3'
Chain IDs:A, B
Chain Length:10
Number of Molecules:2
Biological Source:
Ligand Molecules
MG
PNT
Primary Citation
Coiled-coil conformation of a pentamidine-DNA complex
Acta Crystallogr.,Sect.D 66 251 257 (2010)
PMID: 20179336 DOI: 10.1107/S0907444909055693

Abstact

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.

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Primary Citation of related structures
3EY0