2kbd: Difference between revisions

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{{Seed}}
[[Image:2kbd.png|left|200px]]


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==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'==
The line below this paragraph, containing "STRUCTURE_2kbd", creates the "Structure Box" on the page.
<StructureSection load='2kbd' size='340' side='right'caption='[[2kbd]]' 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'>[[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 [https://proteopedia.org/fgij/fg.htm?mol=2KBD 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">Solution NMR</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2kbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kbd OCA], [https://pdbe.org/2kbd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kbd RCSB], [https://www.ebi.ac.uk/pdbsum/2kbd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kbd ProSAT]</span></td></tr>
{{STRUCTURE_2kbd|  PDB=2kbd  |  SCENE=  }}
</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.


===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'===
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>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
The line below this paragraph, {{ABSTRACT_PUBMED_9636705}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2kbd" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 9636705 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_9636705}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KBD OCA].
[[Category: Delepierre M]]
 
[[Category: Hantz E]]
==Reference==
[[Category: Hartmann B]]
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:[http://www.ncbi.nlm.nih.gov/pubmed/9636705 9636705]
[[Category: Tisne C]]
[[Category: Delepierre, M.]]
[[Category: Hantz, E.]]
[[Category: Hartmann, B.]]
[[Category: Tisne, C.]]
[[Category: Deoxyribonucleic acid]]
[[Category: Dna structure]]
[[Category: Modelling]]
[[Category: Nmr]]
 
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