1cx5
From Proteopedia
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|PDB= 1cx5 |SIZE=350|CAPTION= <scene name='initialview01'>1cx5</scene> | |PDB= 1cx5 |SIZE=350|CAPTION= <scene name='initialview01'>1cx5</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</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>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=MMT:5'-O-(DIMETHYLAMINO)-THYMIDINE'>MMT</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1cx5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cx5 OCA], [http://www.ebi.ac.uk/pdbsum/1cx5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1cx5 RCSB]</span> | ||
}} | }} | ||
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[[Category: nmr]] | [[Category: nmr]] | ||
| - | ''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 19:30:16 2008'' |
Revision as of 16:30, 30 March 2008
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| Ligands: | , , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
ANTISENSE DNA/RNA HYBRID CONTAINING MODIFIED BACKBONE
Overview
The solution structure of an antisense DNA.RNA hybrid duplex, d(CGCGTT-MMI-TTGCGC).r(GCGCAAAACGCG) (designated R4), containing an MMI backbone linker [3'-CH(2)N(CH(3))-O5'], is elucidated. The structural details of the MMI linker, its structural effects on the neighboring residues, and the molecular basis of the MMI effects are examined. The lipophilic N-methyl group of MMI is peripheral to the helix, assuming a conformation that is most stable with regard to the N-O torsion angle. The MMI linker promotes a 3'-endo conformation for the sugar moieties at both 3'- and 5'-adjacent positions and a backbone kink involving distant residues along the 3'-direction. Comparison of R4 with other analogous hybrid duplexes previously studied in this laboratory reveals a new family of low-energy helical conformations that can be accommodated in stable duplexes and a common feature of C3'-modified sugars for adopting a C3'-endo pucker. The results of these studies emphasize the interplay of several factors that govern the formation of stable hybrid duplexes and provide a basis for the understanding of the biological role of the MMI modifications, which are important building blocks for a family of promising chimeric antisense oligonucleotides.
About this Structure
1CX5 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
NMR structure of an antisense DNA.RNA hybrid duplex containing a 3'-CH(2)N(CH(3))-O-5' or an MMI backbone linker., Yang X, Han X, Cross C, Bare S, Sanghvi Y, Gao X, Biochemistry. 1999 Sep 28;38(39):12586-96. PMID:10504227
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