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==XBY6: An analog of CK14 containing 6 dithiophosphate groups==
==XBY6: An analog of CK14 containing 6 dithiophosphate groups==
<StructureSection load='1k8l' size='340' side='right'caption='[[1k8l]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
<StructureSection load='1k8l' size='340' side='right'caption='[[1k8l]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1k8l]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K8L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K8L FirstGlance]. <br>
<table><tr><td colspan='2'>[[1k8l]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K8L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K8L FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2S:CYTIDINE-5-DITHIOPHOSPHORATE'>C2S</scene>, <scene name='pdbligand=G2S:GUANOSINE-5-DITHIOPHOSPHORATE'>G2S</scene>, <scene name='pdbligand=T2S:THYMIDINE-5-DITHIOPHOSPHORATE'>T2S</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1k8j|1k8j]], [[1k8n|1k8n]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2S:CYTIDINE-5-DITHIOPHOSPHORATE'>C2S</scene>, <scene name='pdbligand=G2S:GUANOSINE-5-DITHIOPHOSPHORATE'>G2S</scene>, <scene name='pdbligand=T2S:THYMIDINE-5-DITHIOPHOSPHORATE'>T2S</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1k8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k8l OCA], [https://pdbe.org/1k8l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k8l RCSB], [https://www.ebi.ac.uk/pdbsum/1k8l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k8l ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1k8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k8l OCA], [https://pdbe.org/1k8l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k8l RCSB], [https://www.ebi.ac.uk/pdbsum/1k8l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k8l ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A variety of monothio- and dithiosubstituted duplex aptamers targeting NF-kappaB have been synthesized and designed. The specificity and affinity of the dithioate aptamers of p50 and RelA(p65) NF-kappaB homodimers was determined by gel shift experiments. The NMR solution structures for several unmodified and dithioate backbone modified 14-base paired duplex aptamers have been determined by a hybrid, complete matrix (MORASS)/restrained molecular dynamics method. Structural perturbations of the dithioate substitutions support our hypothesis that the dithioate binds cations less tightly than phosphoryl groups. This increases the electrostatic repulsion across the B-form narrow minor groove and enlarges the minor groove, similar to that found in A-form duplexes. Structural analysis of modeled aptamer complexes with NF-kappaB homo- and heterodimers suggests that the dithioate backbone substitution can increase the aptamer's relative affinity to basic groups in proteins such as NF-kappaB by helping to "strip" the cations from the aptamer backbone.
Solution structure and design of dithiophosphate backbone aptamers targeting transcription factor NF-kappaB.,Volk DE, Yang X, Fennewald SM, King DJ, Bassett SE, Venkitachalam S, Herzog N, Luxon BA, Gorenstein DG Bioorg Chem. 2002 Dec;30(6):396-419. PMID:12642125<ref>PMID:12642125</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1k8l" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Bassett, S E]]
[[Category: Bassett SE]]
[[Category: Fennewald, S M]]
[[Category: Fennewald SM]]
[[Category: Gorenstein, D G]]
[[Category: Gorenstein DG]]
[[Category: Herzog, N]]
[[Category: Herzog N]]
[[Category: King, D J]]
[[Category: King DJ]]
[[Category: Luxon, B A]]
[[Category: Luxon BA]]
[[Category: Venkitachalam, S]]
[[Category: Venkitachalam S]]
[[Category: Volk, D E]]
[[Category: Volk DE]]
[[Category: Yang, X]]
[[Category: Yang X]]
[[Category: Ck1]]
[[Category: Ck14]]
[[Category: Dna]]
[[Category: Nf-kb]]
[[Category: Phosphorodithioate]]
[[Category: Xby6]]
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