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.


3tvb

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:15, 1 March 2024) (edit) (undo)
 
(4 intermediate revisions not shown.)
Line 1: Line 1:
 +
==A Highly Symmetric DNA G-4 Quadruplex/drug Complex==
==A Highly Symmetric DNA G-4 Quadruplex/drug Complex==
-
<StructureSection load='3tvb' size='340' side='right' caption='[[3tvb]], [[Resolution|resolution]] 1.08&Aring;' scene=''>
+
<StructureSection load='3tvb' size='340' side='right'caption='[[3tvb]], [[Resolution|resolution]] 1.08&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3tvb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TVB FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3tvb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TVB FirstGlance]. <br>
-
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DM1:DAUNOMYCIN'>DM1</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.08&#8491;</td></tr>
-
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3tvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tvb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tvb RCSB], [http://www.ebi.ac.uk/pdbsum/3tvb PDBsum]</span></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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-
<table>
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3tvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tvb OCA], [https://pdbe.org/3tvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tvb RCSB], [https://www.ebi.ac.uk/pdbsum/3tvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tvb ProSAT]</span></td></tr>
-
<div style="background-color:#fffaf0;">
+
</table>
-
== Publication Abstract from PubMed ==
+
-
We have determined the X-ray structure of the complex between the DNA quadruplex d(5'-GGGG-3')(4) and daunomycin, as a potential model for studying drug-telomere interactions. The structure was solved at 1.08 A by direct methods in space group I4. The asymmetric unit comprises a linear arrangement of one d(GGGG) strand, four daunomycin molecules, a second d(GGGG) strand facing in the opposite direction to the first, and Na and Mg cations. The crystallographic 4-fold axis generates the biological unit, which is a 12-layered structure comprising two sets of four guanine layers, with four layers each of four daunomycins stacked between the 5' faces of the two quadruplexes. The daunomycin layers fall into two groups which are novel in their mode of self assembly. The only contacts between daunomycin molecules within any one of these layers are van der Waals interactions, however there is substantial pi-pi stacking between successive daunomycin layers and also with adjacent guanine layers. The structure differs significantly from all other parallel d(TGGGGT)(4) quadruplexes in that the 5' guanine adopts the unusual syn glycosyl linkage, refuting the widespread belief that such conformations should all be anti. In contrast to the related d(TGGGGT)/daunomycin complex, there are no ligand-quadruplex groove insertion interactions.
+
-
 
+
-
The high-resolution crystal structure of a parallel intermolecular DNA G-4 quadruplex/drug complex employing syn glycosyl linkages.,Clark GR, Pytel PD, Squire CJ Nucleic Acids Res. 2012 Feb 28. PMID:22373921<ref>PMID:22373921</ref>
+
-
 
+
-
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Clark, G R.]]
+
[[Category: Large Structures]]
-
[[Category: Pytel, P D.]]
+
[[Category: Clark GR]]
-
[[Category: Squire, C J.]]
+
[[Category: Pytel PD]]
-
[[Category: Daunomycin]]
+
[[Category: Squire CJ]]
-
[[Category: Dna-antibiotic complex]]
+
-
[[Category: Dna-drug complex]]
+
-
[[Category: G-4 quadruplex]]
+

Current revision

A Highly Symmetric DNA G-4 Quadruplex/drug Complex

PDB ID 3tvb

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/3tvb"
Personal tools