1D64

CRYSTAL STRUCTURE OF A PENTAMIDINE-OLIGONUCLEOTIDE COMPLEX: IMPLICATIONS FOR DNA-BINDING PROPERTIES

Summary for 1D64

• Entry DOI: 10.2210/pdb1d64/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'), 1,5-BIS(4-AMIDINOPHENOXY)PENTANE (3 entities in total)
• Functional Keywords: b-dna, double helix, complexed with drug, dna
• Total number of polymer chains: 2
• Total formula weight: 7667.20

Authors

Edwards, K.J.,Jenkins, T.C.,Neidle, S. (deposition date: 1992-03-02, release date: 1993-01-15, Last modification date: 2024-02-07)

Primary citation

Edwards, K.J.,Jenkins, T.C.,Neidle, S.
Crystal structure of a pentamidine-oligonucleotide complex: implications for DNA-binding properties.
Biochemistry, 31:7104-7109, 1992

PubMed Abstract: The crystal structure of the complex formed between the dodecanucleotide d(CGCGAATTCGCG)2 and the drug pentamidine, which is active against the Pneumocystis carinii pathogen in AIDS patients, has been determined to a resolution of 2.1 A and an R-factor of 19.4%. Analysis of the structure has shown the drug to be bound in the 5'-AATT minor groove region of the duplex, with the amidinium groups H-bonded to adenine N3 atoms in an interstrand manner. The drug molecule adopts an extended conformation, and the immediate binding site spans four base pairs. Structural details of the drug-DNA interactions are discussed, and comparison is made with the dodecamer complex of the structurally similar berenil ligand.

PubMed: 1643044
DOI: 10.1021/bi00146a011

Experimental method

X-RAY DIFFRACTION (2.1 Å)