1on5
From Proteopedia
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|PDB= 1on5 |SIZE=350|CAPTION= <scene name='initialview01'>1on5</scene> | |PDB= 1on5 |SIZE=350|CAPTION= <scene name='initialview01'>1on5</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CHD:CHOLIC ACID'>CHD</scene> | + | |LIGAND= <scene name='pdbligand=5AT:5'-AMINO-5'-DEOXYTHYMIDINE'>5AT</scene>, <scene name='pdbligand=CHD:CHOLIC+ACID'>CHD</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> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1on5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1on5 OCA], [http://www.ebi.ac.uk/pdbsum/1on5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1on5 RCSB]</span> | ||
}} | }} | ||
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[[Category: Richert, C.]] | [[Category: Richert, C.]] | ||
[[Category: Tuma, J.]] | [[Category: Tuma, J.]] | ||
| - | [[Category: CHD]] | ||
[[Category: dna]] | [[Category: dna]] | ||
[[Category: steroid]] | [[Category: steroid]] | ||
[[Category: synthetic hybrid]] | [[Category: synthetic hybrid]] | ||
| - | ''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 22:47:35 2008'' |
Revision as of 19:47, 30 March 2008
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| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
SOLUTION STRUCTURE OF A CHOLIC ACID-CAPPED DNA DUPLEX
Overview
The three-dimensional structure of a covalent hybrid between cholic acid and the self-complementary DNA hexamer 5'-TGCGCA-3' was solved via two-dimensional NMR and restrained torsion angle molecular dynamics. In the complex, refined to a pairwise rmsd of 0.64 A, the steroid binds to the terminal T:A base pairs via extensive van der Waals contacts but without any hydrogen bonds or detectable dipole-dipole interactions. The contacts involve the methyl groups as well as one edge of the streoid's sterane skeleton and both nucleobases and the deoxyriboses of the terminal base pair of the DNA. The surprising shape complementarity between steroid and the undisturbed DNA termini explains the increase in fidelity and affinity observed for hybridization probes bearing bile acid residues. Since the hydroxyl groups of the steroid do not contribute to the binding of the DNA, they may be derivatized, potentially giving access to a new class of specific binders for blunt ends of Watson-Crick duplexes.
About this Structure
1ON5 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of a steroid-DNA complex with cholic acid residues sealing the termini of a Watson-Crick duplex., Tuma J, Richert C, Biochemistry. 2003 Aug 5;42(30):8957-65. PMID:12885228
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