1G3X

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

Summary for 1G3X

• Entry DOI: 10.2210/pdb1g3x/pdb
• Descriptor: 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)
• Functional Keywords: dna, drug-peptide adduct, intercalation, mg+2 ions
• Total number of polymer chains: 13
• Total formula weight: 44982.84

Authors

Malinina, L.,Soler-Lopez, M.,Aymami, J.,Subirana, J.A. (deposition date: 2000-10-25, release date: 2002-08-16, Last modification date: 2024-10-30)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.7 Å)