1db6
From Proteopedia
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|PDB= 1db6 |SIZE=350|CAPTION= <scene name='initialview01'>1db6</scene> | |PDB= 1db6 |SIZE=350|CAPTION= <scene name='initialview01'>1db6</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=AAR:ARGININEAMIDE'>AAR</scene> | + | |LIGAND= <scene name='pdbligand=AAR:ARGININEAMIDE'>AAR</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2arg|2ARG]], [[1old|1OLD]] | ||
| + | |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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[[Category: Robertson, S A.]] | [[Category: Robertson, S A.]] | ||
[[Category: Wemmer, D E.]] | [[Category: Wemmer, D E.]] | ||
| - | [[Category: AAR]] | ||
[[Category: aptamer]] | [[Category: aptamer]] | ||
[[Category: argininamide]] | [[Category: argininamide]] | ||
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[[Category: single-strand]] | [[Category: single-strand]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:38:09 2008'' |
Revision as of 16:38, 30 March 2008
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| Ligands: | , , , , | ||||||
| Related: | 2ARG, 1OLD
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE
Overview
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.
About this Structure
1DB6 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Sun Mar 30 19:38:09 2008
Categories: Protein complex | Frankel, A D. | Harada, K. | Robertson, S A. | Wemmer, D E. | Aptamer | Argininamide | Arginine | Hairpin | Nmr | Selex | Single-strand
