375D

A NOVEL END-TO-END BINDING OF TWO NETROPSINS TO THE DNA DECAMER D(CCCCCIIIII)2

375D の概要

• エントリーDOI: 10.2210/pdb375d/pdb
• 分子名称: DNA (5'-D(*CP*CP*CP*CP*CP*IP*IP*IP*IP*I)-3'), NETROPSIN (3 entities in total)
• 機能のキーワード: unusual dna/rna, double helix, double drug in minor groove, complexed with drug, mismatched, dna
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 13609.50

構造登録者

Chen, X.,Rao, S.T.,Sekar, K.,Sundaralingam, M. (登録日: 1998-01-14, 公開日: 1998-12-02, 最終更新日: 2024-02-21)

主引用文献

Chen, X.,Mitra, S.N.,Rao, S.T.,Sekar, K.,Sundaralingam, M.
A Novel End-to-End Binding of Two Netropsins to the DNA Decamers d(CCCCCIIIII) 2, d(CCCBr5CCIIIII)2, d(CBr5CCCCIIIII)2
Nucleic Acids Res., 26:5464-5471, 1998

PubMed Abstract: Netropsin is bound to the DNA decamer d(CCCCCIIIII)2, the C-4 bromo derivative d(CCCBr5CCIIIII)2and the C-2 bromo derivative d(CBr5CCCCIIIII)2in a novel 2:1 mode. Complexes of the native decamer and the C-4 bromo derivative are isomorphous, space group P1, unit cell dimensions a = 32.56 A (32.66), b = 32.59 A (32.77), c = 37.64 A (37.71), alpha = 86.30 degrees (86.01 degrees), beta = 84.50 degrees (84.37 degrees), gamma = 68.58 degrees (68.90 degrees) with two independent molecules (A and B) in the asymmetric unit (values in parentheses are for the derivative). The C-2 bromo derivative is hexagonal P61, unit cell dimensions a = b = 32.13 A, c = 143.92, gamma = 120 degrees with one molecule in the asymmetric unit. The structures were solved by the molecular replacement method. The novelty of the structures is that there are two netropsins bound end-to-end in the minor groove of each B-DNA decamer which has nearly a complete turn. The netropsins are held by hydrogen bonding interactions to the base atoms and by sandwiching van der Waal's interactions from the sugar-phosphate backbones of the double helix similar to every other drug.DNA complex. Each netropsin molecule spans approximately 5 bp. The netropsins refined with their guanidinium heads facing each other at the center, although an orientational disorder for the netropsins cannot be excluded. The amidinium ends stretch out toward the junctions and bind to the adjacent duplexes in the columns of stacked symmetry-related complexes. Both cationic ends of netropsin are bridged by water molecules in one of the independent molecules (molecule A) of the triclinic structures and also the hexagonal structure to form pseudo-continuous drug.decamer helices.

PubMed: 9826773
DOI: 10.1093/nar/26.23.5464

実験手法

X-RAY DIFFRACTION (2.4 Å)