1G3X

INTERCALATION OF AN 9ACRIDINE-PEPTIDE DRUG IN A DNA DODECAMER

1G3X の概要

• エントリーDOI: 10.2210/pdb1g3x/pdb
• 分子名称: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', N(ALPHA)-(9-ACRIDINOYL)-TETRAARGININE-AMIDE, MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: dna, drug-peptide adduct, intercalation, mg+2 ions
• タンパク質・核酸の鎖数: 13
• 化学式量合計: 44982.84

構造登録者

Malinina, L.,Soler-Lopez, M.,Aymami, J.,Subirana, J.A. (登録日: 2000-10-25, 公開日: 2002-08-16, 最終更新日: 2024-10-30)

主引用文献

Malinina, L.,Soler-Lopez, M.,Aymami, J.,Subirana, J.A.
Intercalation of an acridine-peptide drug in an AA/TT base step in the crystal structure of [d(CGCGAATTCGCG)](2) with six duplexes and seven Mg(2+) ions in the asymmetric unit.
Biochemistry, 41:9341-9348, 2002

PubMed Abstract: We present the crystal structure of an acridine drug derivatized at carbon 9, [N(alpha)-(9-acridinoyl)-tetraarginine], intercalated within the dodecamer [d(CGCGAATTCGCG)](2). The presence of a lateral chain at the central carbon 9 atom differentiates this compound from most acridine drugs hitherto studied, which are usually derivatized at carbon 4. The DNA:drug interaction we observe differs from that observed in previous studies, which primarily involves shorter, mainly hexameric sequences, in two important regards: the acridine intercalates within an AA/TT base step, rather than within a CG/CG base step; and the binding site is located at the center of the sequence, rather than at one end of the duplex. In addition, we observe a novel crystal packing arrangement, with six dodecamer duplexes and seven hydrated magnesium ions in the asymmetric unit of a large (66.5 x 68.4 x 77.4 A(3)) unit cell in space group P2(1)2(1)2(1). The duplexes are organized in layers parallel to the ab plane, with consecutive layers crossing each other at right angles.

PubMed: 12135355
DOI: 10.1021/bi020135c

実験手法

X-RAY DIFFRACTION (2.7 Å)