1prp
From Proteopedia
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CRYSTAL STRUCTURE OF D(CGCGAATTCGCG) COMPLEXED WITH PROPAMIDINE, A SHORT-CHAIN HOMOLOGUE OF THE DRUG PENTAMIDIN
Overview
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.
About this Structure
1PRP is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Crystal structure of d(CGCGAATTCGCG) complexed with propamidine, a short-chain homologue of the drug pentamidine., Nunn CM, Jenkins TC, Neidle S, Biochemistry. 1993 Dec 21;32(50):13838-43. PMID:8268158
Page seeded by OCA on Thu Feb 21 14:31:51 2008
