ISDA

Entry Detail

PDB ID:

159D

Keywords:

DNA

Title:

SIDE BY SIDE BINDING OF TWO DISTAMYCIN A DRUGS IN THE MINOR GROOVE OF AN ALTERNATING B-DNA DUPLEX

Biological Source:

Source Organism:

PDB Version:

Deposition Date:

1994-02-10

Release Date:

1995-02-07

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.80 Å

R-Value Work:

0.15

R-Value Observed:

0.15

Space Group:

P 41 2 2

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Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*IP*CP*IP*CP*IP*CP*IP*C)-3')
Chain IDs:A
Chain Length:8
Number of Molecules:1
Biological Source:

Ligand Molecules

DMY

Primary Citation

Binding of two distamycin A molecules in the minor groove of an alternating B-DNA duplex.

Chen, X, Ramakrishnan, B, Rao, S.T, Sundaralingam, M.Show

Nat.Struct.Biol. 1 169 175 (1994)

PMID: 7656035 DOI: 10.1038/nsb0394-169

Abstact

Here we report the 1.8A X-ray structure of a 2:1 drug-DNA complex between distamycin A and an alternating B-DNA octamer duplex d(ICICICIC)2. The two distamycin A molecules are bound side by side with dyad symmetry in an antiparallel orientation in the expanded minor groove. The amides of each drug molecule are hydrogen bonded to the minor groove base atoms of only one DNA strand. The complex not only shows binding of two drug molecules, but the DNA duplex also exhibits striking low-high alternations in the helical twist angles, the sugar puckering and the phosphate conformations, providing the basis for a new model for an alternating B-DNA with a dinucleotide repeat.

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Protein

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Disease

Primary Citation of related structures