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481d
From Proteopedia
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|PDB= 481d |SIZE=350|CAPTION= <scene name='initialview01'>481d</scene>, resolution 1.60Å | |PDB= 481d |SIZE=350|CAPTION= <scene name='initialview01'>481d</scene>, resolution 1.60Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=6HA:1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(ADENIN-9-YL)-6'-O-PHOSPHORYL-D-ARABINO-HEXITOL'>6HA</scene>, <scene name='pdbligand=6HC:1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(CYTOSIN-1-YL)-6'-O-PHOSPHORYL-D-ARABINO-HEXITOL'>6HC</scene>, <scene name='pdbligand=6HG:1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(GUANIN-9-YL)-6'-O-PHOSPHORYL-D-ARABINO-HEXITOL'>6HG</scene>, <scene name='pdbligand=6HT:1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(THYMIN-1-YL)-6'-O-PHOSPHORYL-D-ARABINO-HEXITOL'>6HT</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=481d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=481d OCA], [http://www.ebi.ac.uk/pdbsum/481d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=481d RCSB]</span> | ||
}} | }} | ||
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[[Category: hexitol nucleic acid]] | [[Category: hexitol nucleic acid]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:37:46 2008'' |
Revision as of 02:37, 31 March 2008
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| , resolution 1.60Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF A HEXITOL NUCLEIC ACID (HNA) DUPLEX AT 1.6A RESOLUTION
Overview
A huge variety of chemically modified oligonucleotide derivatives has been synthesized for possible antisense applications. One such derivative, hexitol nucleic acid (HNA), is a DNA analogue containing the standard nucleoside bases, but with a phosphorylated 1',5'-anhydrohexitol backbone. Hexitol nucleic acids are some of the strongest hybridizing antisense compounds presently known, but HNA duplexes are even more stable. We present here the first high-resolution structure of a double helical nucleic acid with all sugars being hexitols. Although designed to have a restricted conformational flexibility, the hexitol oligomer h(GTGTACAC) is able to crystallize in two different double helical conformations. Both structures display a high x-displacement, normal Watson-Crick base pairing, similar base stacking patterns, and a very deep major groove together with a minor groove with increased hydrophobicity. One of the conformations displays a major groove which is wide enough to accommodate a second HNA double helix resulting in the formation of a double helix of HNA double helices. Both structures show most similarities with the A-type helical structure, the anhydrohexitol chair conformation thereby acting as a good mimic for the furanose C3'-endo conformation observed in RNA. As compared to the quasi-linear structure of homo-DNA, the axial position of the base in HNA allows efficient base stacking and hence double helix formation.
About this Structure
481D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Crystal structure of double helical hexitol nucleic acids., Declercq R, Van Aerschot A, Read RJ, Herdewijn P, Van Meervelt L, J Am Chem Soc. 2002 Feb 13;124(6):928-33. PMID:11829600
Page seeded by OCA on Mon Mar 31 05:37:46 2008
