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.


2dnd

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:18, 14 February 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2dnd.jpg|left|200px]]
 
-
<!--
+
==A BIFURCATED HYDROGEN-BONDED CONFORMATION IN THE D(A.T) BASE PAIRS OF THE DNA DODECAMER D(CGCAAATTTGCG) AND ITS COMPLEX WITH DISTAMYCIN==
-
The line below this paragraph, containing "STRUCTURE_2dnd", creates the "Structure Box" on the page.
+
<StructureSection load='2dnd' size='340' side='right'caption='[[2dnd]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[2dnd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DND OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DND FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMY:DISTAMYCIN+A'>DMY</scene></td></tr>
-
{{STRUCTURE_2dnd| PDB=2dnd | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dnd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dnd OCA], [https://pdbe.org/2dnd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dnd RCSB], [https://www.ebi.ac.uk/pdbsum/2dnd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dnd ProSAT]</span></td></tr>
-
 
+
</table>
-
'''A BIFURCATED HYDROGEN-BONDED CONFORMATION IN THE D(A.T) BASE PAIRS OF THE DNA DODECAMER D(CGCAAATTTGCG) AND ITS COMPLEX WITH DISTAMYCIN'''
+
__TOC__
-
 
+
</StructureSection>
-
 
+
[[Category: Large Structures]]
-
==Overview==
+
[[Category: Coll M]]
-
The crystal structures of d(CGCA3T3GCG) complex to the antitumor drug distamycin and the DNA fragment alone were solved by x-ray diffraction at 2.2 and 2.5 A resolution, respectively. The drug lies in the narrow minor groove near the center of the B-DNA fragment covering 5 of the 6 A.T base pairs. It is bound to the DNA by hydrogen bonding, van der Waals, and electrostatic interactions. In addition, the DNA was found to have an unusual conformation in the (dA)3.(dT)3 regions. These base pairs have a high positive propeller twist so that in the major groove the adenine amino group is located intermediate between the carbonyl O-4 groups of two adjacent thymines of the opposite strand, making bifurcated hydrogen bonds to the two thymine residues. This suggests a model to explain the unusual properties of poly-(dA).poly(dT) in which a modified B conformation is associated with a large propeller twist of the bases and a set of continuous bifurcating hydrogen bonds along the major groove, which may provide incremental stability to these segments. In addition, shorter segments of (dA)3-6.(dT)3-6 may have this conformation in the midst of B-DNA and stabilize bends in the DNA that may be associated with stacking on one of the high propeller-twisted bases at the ends of these segments.
+
[[Category: Frederick CA]]
-
 
+
[[Category: Rich A]]
-
==About this Structure==
+
[[Category: Wang AH-J]]
-
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DND OCA].
+
-
 
+
-
==Reference==
+
-
A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin., Coll M, Frederick CA, Wang AH, Rich A, Proc Natl Acad Sci U S A. 1987 Dec;84(23):8385-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/3479798 3479798]
+
-
[[Category: Coll, M.]]
+
-
[[Category: Frederick, C A.]]
+
-
[[Category: Rich, A.]]
+
-
[[Category: Wang, A H.J.]]
+
-
[[Category: B-dna]]
+
-
[[Category: Complexed with drug]]
+
-
[[Category: Double helix]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 00:48:16 2008''
+

Current revision

A BIFURCATED HYDROGEN-BONDED CONFORMATION IN THE D(A.T) BASE PAIRS OF THE DNA DODECAMER D(CGCAAATTTGCG) AND ITS COMPLEX WITH DISTAMYCIN

PDB ID 2dnd

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/2dnd"
Personal tools