PDBsum entry 1vti

DNA

PDB id

1vti

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Contents

			DNA/RNA

			Ligands

					DM1

			Waters ×52

PDB id:

1vti

Links

Name:

DNA

Title:

DNA-drug interactions: the crystal structures of d(tgatca) complexed with daunomycin

Structure:

DNA (5'-d( Tp Gp Tp Ap Cp A)-3'). Chain: a. Engineered: yes

Source:

Synthetic: yes

Resolution:

1.70Å

R-factor:

0.260

Authors:

C.M.Nunn,L.Van Meervelt,S.Zhang,M.H.Moore,O.Kennard

Key ref:

C.M.Nunn et al. (1991). DNA-drug interactions. The crystal structures of d(TGTACA) and d(TGATCA) complexed with daunomycin. J Mol Biol, 222, 167-177. PubMed id: 1960720

Date:

01-Mar-92

Release date:

13-Jul-11

	Headers

	References

DNA/RNA chain

T-G-A-T-C-A 6 bases

	J Mol Biol 222:167-177 (1991)
PubMed id: 1960720

DNA-drug interactions. The crystal structures of d(TGTACA) and d(TGATCA) complexed with daunomycin.
C.M.Nunn, L.Van Meervelt, S.D.Zhang, M.H.Moore, O.Kennard.

ABSTRACT

The anticancer drug daunomycin has been co-crystallized with the hexanucleotide duplex sequences d(TGTACA) and d(TGATCA) and single crystal X-ray diffraction studies of these two complexes have been carried out. Structure solution of the d(TGTACA) and d(TGATCA) complexes to 1.6 and 1.7 Angstrom resolution, respectively, shows two daunomycin molecules bound to the DNA hexamer. Binding occurs via intercalation of the drug chromophore at the d(TpG) step, and hydrogen bonding interactions involving the drug, DNA and solvent molecules. The daunomycin sugar is located in the minor groove of the DNA hexamer and is stabilized by hydrogen bonds between the amino group of the sugar and functional groups on the floor of the groove. The amino sugar of the d(TGATCA) duplex interacts directly with the DNA sequence, while in the d(TGTACA) duplex, the interaction is via solvent molecules. Two other complexes d(CGTACG)-daunomycin and d(CGATCG)-daunomycin have previously been structurally characterized. Comparison of the four structures with daunomycin bound to the triplet sequences 5'TGT, 5'TGA, 5'CGT and 5'CGA reveals changes in the conformation of both the DNA hexamer and the daunomycin upon complexation, as well as the hydrogen bonding and van der Waals' interactions.

Literature references that cite this PDB file's key reference

PubMed id

Reference

12876339

K.Shi, B.Pan, and M.Sundaralingam (2003).
Structure of a B-form DNA/RNA chimera (dC)(rG)d(ATCG) complexed with daunomycin at 1.5 A resolution.

Acta Crystallogr D Biol Crystallogr, 59, 1377-1383.

PDB code:

1jo2

8662899

W.B.Cruse, P.Saludjian, Y.Leroux, G.Léger, D.E.Manouni, and T.Prangé (1996).
A continuous transition from A-DNA to B-DNA in the 1:1 complex between nogalamycin and the hexamer dCCCGGG.

J Biol Chem, 271, 15558-15567.

PDB code:

282d

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