1da0
From Proteopedia
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|PDB= 1da0 |SIZE=350|CAPTION= <scene name='initialview01'>1da0</scene>, resolution 1.500Å | |PDB= 1da0 |SIZE=350|CAPTION= <scene name='initialview01'>1da0</scene>, resolution 1.500Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=DM1:DAUNOMYCIN'>DM1</scene> | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DM1:DAUNOMYCIN'>DM1</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1da0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1da0 OCA], [http://www.ebi.ac.uk/pdbsum/1da0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1da0 RCSB]</span> | ||
}} | }} | ||
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[[Category: Kennard, O.]] | [[Category: Kennard, O.]] | ||
[[Category: Moore, M H.]] | [[Category: Moore, M H.]] | ||
| - | [[Category: DM1]] | ||
[[Category: complexed with drug]] | [[Category: complexed with drug]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
[[Category: right handed dna]] | [[Category: right handed dna]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:37:36 2008'' |
Revision as of 16:37, 30 March 2008
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| , resolution 1.500Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
DNA-DRUG INTERACTIONS: THE CRYSTAL STRUCTURE OF D(CGATCG) COMPLEXED WITH DAUNOMYCIN
Overview
The structure of a d(CGATCG)-daunomycin complex has been determined by single crystal X-ray diffraction techniques. Refinement, with the location of 40 solvent molecules, using data up to 1.5 A, converged with a final crystallographic residual, R = 0.25 (RW = 0.22). The tetragonal crystals are in space group P4(1)2(1)2, with cell dimensions of a = 27.98 A and c = 52.87 A. The self-complementary d(CGATCG) forms a distorted right-handed helix with a daunomycin molecule intercalated at each d(CpG) step. The daunomycin aglycon chromophore is oriented at right-angles to the long axis of the DNA base-pairs. This head-on intercalation is stabilized by direct hydrogen bonds and indirectly via solvent-mediated, hydrogen-bonding interactions between the chromophore and its intercalation site base-pairs. The cyclohexene ring and amino sugar substituent lie in the minor groove. The amino sugar N-3' forms a hydrogen bond with O-2 of the next neighbouring thymine. This electrostatic interaction helps position the sugar in a way that results in extensive van der Waals contacts between the drug and the DNA. There is no interaction between daunosamine and the DNA sugar-phosphate backbone. We present full experimental details and all relevant conformational parameters, and use the comparison with a d(CGTACG)-daunomycin complex to rationalize some neighbouring sequence effects involved in daunomycin binding.
About this Structure
1DA0 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
DNA-drug interactions. The crystal structure of d(CGATCG) complexed with daunomycin., Moore MH, Hunter WN, d'Estaintot BL, Kennard O, J Mol Biol. 1989 Apr 20;206(4):693-705. PMID:2738914
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