1ddy
From Proteopedia
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|PDB= 1ddy |SIZE=350|CAPTION= <scene name='initialview01'>1ddy</scene>, resolution 3.0Å | |PDB= 1ddy |SIZE=350|CAPTION= <scene name='initialview01'>1ddy</scene>, resolution 3.0Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=B12:COBALAMIN'>B12</scene> | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=NME:METHYLAMINE'>NME</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ddy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ddy OCA], [http://www.ebi.ac.uk/pdbsum/1ddy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ddy RCSB]</span> | ||
}} | }} | ||
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[[Category: Sussman, D.]] | [[Category: Sussman, D.]] | ||
[[Category: Wilson, C.]] | [[Category: Wilson, C.]] | ||
| - | [[Category: B12]] | ||
| - | [[Category: NME]] | ||
[[Category: aptamer]] | [[Category: aptamer]] | ||
[[Category: rna]] | [[Category: rna]] | ||
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[[Category: vitamin b12]] | [[Category: vitamin b12]] | ||
| - | ''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 19:39:43 2008'' |
Revision as of 16:39, 30 March 2008
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| , resolution 3.0Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
MOLECULAR RECOGNITION BY THE VITAMIN B12 RNA APTAMER
Overview
Previous solution structures of ligand-binding RNA aptamers have shown that molecular recognition is achieved by the folding of an initially unstructured RNA around its cognate ligand, coupling the processes of RNA folding and binding. The 3 A crystal structure of the cyanocobalamin (vitamin B12) aptamer reported here suggests a different approach to molecular recognition in which elements of RNA secondary structure combine to create a solvent-accessible docking surface for a large, complex ligand. Central to this structure is a locally folding RNA triplex, stabilized by a novel three-stranded zipper. Perpendicular stacking of a duplex on this triplex creates a cleft that functions as the vitamin B12 binding site. Complementary packing of hydrophobic surfaces, direct hydrogen bonding and dipolar interactions between the ligand and the RNA appear to contribute to binding. The nature of the interactions that stabilize complex formation and the possible uncoupling of folding and binding for this RNA suggest a strong mechanistic similarity to typical protein-ligand complexes.
About this Structure
1DDY is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
The structural basis for molecular recognition by the vitamin B 12 RNA aptamer., Sussman D, Nix JC, Wilson C, Nat Struct Biol. 2000 Jan;7(1):53-7. PMID:10625428
Page seeded by OCA on Sun Mar 30 19:39:43 2008
Categories: Protein complex | Nix, J C. | Sussman, D. | Wilson, C. | Aptamer | Rna | Triplex | Vitamin b12
