1d7z: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1d7z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D7Z FirstGlance]. <br>
<table><tr><td colspan='2'>[[1d7z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D7Z FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><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></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.21&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7z OCA], [https://pdbe.org/1d7z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d7z RCSB], [https://www.ebi.ac.uk/pdbsum/1d7z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d7z ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7z OCA], [https://pdbe.org/1d7z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d7z RCSB], [https://www.ebi.ac.uk/pdbsum/1d7z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d7z ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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<ref>PMID:11829600</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1d7z" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Declercq, R]]
[[Category: Declercq R]]
[[Category: Meervelt, L Van]]
[[Category: Van Meervelt L]]
[[Category: Dna]]
[[Category: Dna analogue]]
[[Category: Double helix]]
[[Category: Hexitol nucleic acid]]

Latest revision as of 06:50, 7 February 2024

CRYSTAL STRUCTURE OF A HEXITOL NUCLEIC ACID (HNA) DUPLEX AT 2.2 A RESOLUTION

1d7z, resolution 2.21Å

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