2kbd: Difference between revisions

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[[Image:2kbd.png|left|200px]]
==5'-D(*CP*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*CP*AP*G)-3'==
<StructureSection load='2kbd' size='340' side='right' caption='[[2kbd]], [[NMR_Ensembles_of_Models | 3 NMR models]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2kbd]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KBD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KBD FirstGlance]. <br>
</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=2kbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kbd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kbd RCSB], [http://www.ebi.ac.uk/pdbsum/2kbd PDBsum]</span></td></tr>
<table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
1H and 31P NMR spectroscopy have been used together with molecular modelling to determine the fine structure of a non-palindromic 16 bp DNA containing the NF-kappa B binding site. Much emphasis has been placed upon NMR optimization of both two-dimensional 31P NMR techniques to extract structural information defining the phosphodiester backbone conformation and selective homonuclear 2D COSY experiments to determine sugar conformations. NMR data show evidence for a dynamic behaviour of steps flanking the ten base-pairs of the NF-kappa B binding site. A BI-BII equilibrium at these steps is demonstrated and two models for each extreme conformation are proposed in agreement with NMR data. In the refined BII structures, the NF-kappa B binding site exhibits an intrinsic curvature towards the major groove that is magnified by the four flanking steps in the BII conformation. Furthermore, the base-pairs are translated into the major groove. Thus, we present a novel mode of dynamic intrinsic curvature compatible with the DNA curvature observed in the X-ray structure of the p50-DNA complex.


{{STRUCTURE_2kbd|  PDB=2kbd  |  SCENE=  }}
Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 kappa B site: evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex.,Tisne C, Hantz E, Hartmann B, Delepierre M J Mol Biol. 1998 May 29;279(1):127-42. PMID:9636705<ref>PMID:9636705</ref>


===5'-D(*CP*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*CP*AP*G)-3'===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_9636705}}
== References ==
 
<references/>
==About this Structure==
__TOC__
[[2kbd]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KBD OCA].
</StructureSection>
 
==Reference==
<ref group="xtra">PMID:009636705</ref><ref group="xtra">PMID:010194299</ref><references group="xtra"/>
[[Category: Delepierre, M.]]
[[Category: Delepierre, M.]]
[[Category: Hantz, E.]]
[[Category: Hantz, E.]]
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