1PRP image
Deposition Date 1993-07-23
Release Date 1994-01-15
Last Version Date 2024-02-14
Entry Detail
PDB ID:
1PRP
Keywords:
DNA
Title:
CRYSTAL STRUCTURE OF D(CGCGAATTCGCG) COMPLEXED WITH PROPAMIDINE, A SHORT-CHAIN HOMOLOGUE OF THE DRUG PENTAMIDIN
Biological Source:
Source Organism:
(Taxon ID: ) (Taxon ID: )
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.10 Å
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 21 21 21
1PRP validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
Chain IDs:A, B
Chain Length:12
Number of Molecules:2
Biological Source:
Ligand Molecules
TNT
Primary Citation
Crystal structure of d(CGCGAATTCGCG) complexed with propamidine, a short-chain homologue of the drug pentamidine.
Biochemistry 32 13838 13843 (1993)
PMID: 8268158 DOI: 10.1021/bi00213a012

Abstact

The crystal structure of the complex between propamidine and the self-complementary DNA dodecamer d(CGCGAATTCGCG) duplex has been determined to a resolution of 2.1 A and a R-factor of 17.4%. The propamidine binds to the DNA within the minor groove, with specific hydrogen-bonding interactions from the amidinium groups to the bases and sugar groups of the DNA, via a 4-base-pair binding site. A network of water molecules lies over the mouth of the minor groove. The structure provides a rationale for the superior DNA-binding properties of propamidine as compared to pentamidine [cf. Edwards, K. J., Jenkins, T. C. & Neidle, S. (1992) Biochemistry 31, 7104-7109]. This is seen to result from (i) decreased minor groove width at the binding site and (ii) reduced mobility of the bound propamidine molecule.

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Primary Citation of related structures
1PRP