1D64 image
Deposition Date 1992-03-02
Release Date 1993-01-15
Last Version Date 2024-02-07
Entry Detail
PDB ID:
1D64
Keywords:
DNA
Title:
CRYSTAL STRUCTURE OF A PENTAMIDINE-OLIGONUCLEOTIDE COMPLEX: IMPLICATIONS FOR DNA-BINDING PROPERTIES
Biological Source:
Source Organism:
(Taxon ID: ) (Taxon ID: )
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.10 Å
R-Value Observed:
0.19
Space Group:
P 21 21 21
1D64 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
PNT
Primary Citation
Crystal structure of a pentamidine-oligonucleotide complex: implications for DNA-binding properties.
Biochemistry 31 7104 7109 (1992)
PMID: 1643044 DOI: 10.1021/bi00146a011

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
1D64