This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1da0

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:51, 7 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1da0.gif|left|200px]]<br /><applet load="1da0" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1da0, resolution 1.500&Aring;" />
 
-
'''DNA-DRUG INTERACTIONS: THE CRYSTAL STRUCTURE OF D(CGATCG) COMPLEXED WITH DAUNOMYCIN'''<br />
 
-
==Overview==
+
==DNA-DRUG INTERACTIONS: THE CRYSTAL STRUCTURE OF D(CGATCG) COMPLEXED WITH DAUNOMYCIN==
-
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.
+
<StructureSection load='1da0' size='340' side='right'caption='[[1da0]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1da0]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DA0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DA0 FirstGlance]. <br>
-
1DA0 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=DM1:'>DM1</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DA0 OCA].
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DM1:DAUNOMYCIN'>DM1</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1da0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1da0 OCA], [https://pdbe.org/1da0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1da0 RCSB], [https://www.ebi.ac.uk/pdbsum/1da0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1da0 ProSAT]</span></td></tr>
-
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2738914 2738914]
+
</table>
-
[[Category: Protein complex]]
+
__TOC__
-
[[Category: Estaintot, B Langlois D.]]
+
</StructureSection>
-
[[Category: Hunter, W N.]]
+
[[Category: Large Structures]]
-
[[Category: Kennard, O.]]
+
[[Category: Hunter WN]]
-
[[Category: Moore, M H.]]
+
[[Category: Kennard O]]
-
[[Category: DM1]]
+
[[Category: Langlois D'Estaintot B]]
-
[[Category: complexed with drug]]
+
[[Category: Moore MH]]
-
[[Category: double helix]]
+
-
[[Category: right handed dna]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:14:30 2008''
+

Current revision

DNA-DRUG INTERACTIONS: THE CRYSTAL STRUCTURE OF D(CGATCG) COMPLEXED WITH DAUNOMYCIN

PDB ID 1da0

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1da0"
Personal tools