2kbd: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image:2kbd.gif|left|200px]] | [[Image:2kbd.gif|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'''' | {{Structure | ||
|PDB= 2kbd |SIZE=350|CAPTION= <scene name='initialview01'>2kbd</scene> | |||
|SITE= | |||
|LIGAND= | |||
|ACTIVITY= | |||
|GENE= | |||
}} | |||
'''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'''' | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
2KBD is a [ | 2KBD is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KBD OCA]. | ||
==Reference== | ==Reference== | ||
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:// | 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: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Delepierre, M.]] | [[Category: Delepierre, M.]] | ||
| Line 21: | Line 30: | ||
[[Category: nmr]] | [[Category: nmr]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:46:16 2008'' | ||
Revision as of 15:46, 20 March 2008
| |||||||||||||
| 2kbd | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
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'
Overview
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.
About this Structure
2KBD is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Thu Mar 20 17:46:16 2008
