1db6

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[[Image:1db6.gif|left|200px]]
 
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{{Structure
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==SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE==
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|PDB= 1db6 |SIZE=350|CAPTION= <scene name='initialview01'>1db6</scene>
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<StructureSection load='1db6' size='340' side='right'caption='[[1db6]]' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=AAR:ARGININEAMIDE'>AAR</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
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<table><tr><td colspan='2'>[[1db6]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DB6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DB6 FirstGlance]. <br>
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|ACTIVITY=
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</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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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AAR:ARGININEAMIDE'>AAR</scene></td></tr>
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|DOMAIN=
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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=1db6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1db6 OCA], [https://pdbe.org/1db6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1db6 RCSB], [https://www.ebi.ac.uk/pdbsum/1db6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1db6 ProSAT]</span></td></tr>
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|RELATEDENTRY=[[2arg|2ARG]], [[1old|1OLD]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1db6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1db6 OCA], [http://www.ebi.ac.uk/pdbsum/1db6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1db6 RCSB]</span>
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<div style="background-color:#fffaf0;">
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}}
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== Publication Abstract from PubMed ==
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'''SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE'''
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==Overview==
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The structure of a DNA aptamer, which was selected for specific binding to arginine, was determined using NMR spectroscopy. The sequence forms a hairpin loop, with residues important for binding occurring in the loop region. Binding of argininamide induces formation of one Watson-Crick and two non-Watson-Crick base pairs, which facilitate generation of a binding pocket. The specificity for arginine seems to arise from contacts between the guanidino end of the arginine and phosphates, with atoms positioned by the shape of the pocket. Complex binding kinetics are observed suggesting that there is a slow interconversion of two forms of the DNA, which have different binding affinities. These data provide information on the process of adaptive recognition of a ligand by an aptamer.
The structure of a DNA aptamer, which was selected for specific binding to arginine, was determined using NMR spectroscopy. The sequence forms a hairpin loop, with residues important for binding occurring in the loop region. Binding of argininamide induces formation of one Watson-Crick and two non-Watson-Crick base pairs, which facilitate generation of a binding pocket. The specificity for arginine seems to arise from contacts between the guanidino end of the arginine and phosphates, with atoms positioned by the shape of the pocket. Complex binding kinetics are observed suggesting that there is a slow interconversion of two forms of the DNA, which have different binding affinities. These data provide information on the process of adaptive recognition of a ligand by an aptamer.
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==About this Structure==
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Structure determination and binding kinetics of a DNA aptamer-argininamide complex.,Robertson SA, Harada K, Frankel AD, Wemmer DE Biochemistry. 2000 Feb 8;39(5):946-54. PMID:10653638<ref>PMID:10653638</ref>
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1DB6 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=1DB6 OCA].
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==Reference==
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Structure determination and binding kinetics of a DNA aptamer-argininamide complex., Robertson SA, Harada K, Frankel AD, Wemmer DE, Biochemistry. 2000 Feb 8;39(5):946-54. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10653638 10653638]
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[[Category: Protein complex]]
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[[Category: Frankel, A D.]]
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[[Category: Harada, K.]]
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[[Category: Robertson, S A.]]
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[[Category: Wemmer, D E.]]
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[[Category: aptamer]]
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[[Category: argininamide]]
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[[Category: arginine]]
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[[Category: hairpin]]
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[[Category: nmr]]
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[[Category: selex]]
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[[Category: single-strand]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:38:09 2008''
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1db6" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Frankel AD]]
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[[Category: Harada K]]
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[[Category: Robertson SA]]
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[[Category: Wemmer DE]]

Current revision

SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE

PDB ID 1db6

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