1zjg: Difference between revisions
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< | ==13mer-co== | ||
<StructureSection load='1zjg' size='340' side='right'caption='[[1zjg]], [[Resolution|resolution]] 3.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1zjg]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZJG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZJG FirstGlance]. <br> | |||
or | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3Å</td></tr> | ||
- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=1zjg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zjg OCA], [https://pdbe.org/1zjg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zjg RCSB], [https://www.ebi.ac.uk/pdbsum/1zjg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zjg ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Three crystal structures containing the entire Sp1 consensus sequence d(GGGGCGGGG) with two or three additional base-pairs on either the 5' or 3' ends and overhangs have been determined. Despite the different lengths of DNA in the pseudo-dodecamers and pseudo-tridecamer, all three structures form A-DNA duplexes that share a common set of crystal contacts, including a T*(G.C) base triplet and a 5'-overhang that flips out and away from the helical axes to form a Hoogsteen base-pair with the 3'-overhang of a symmetry mate. The global conformations of the three structures differ, however, in the widths of their respective major grooves, the lengths of the molecules, and the extent of crystal packing. The structures were determined from crystals grown in an unusual precipitant for A-DNA, polyethylene glycol (PEG) 400, in combination with polyamines or ions; cobalt hexamine for the pseudo-tridecamer, and spermidine for the pseudo-dodecamers. As the Sp1 binding site is a target for antiviral and anticancer drugs, pseudo-dodecamer crystals were soaked with one such antiviral and anticancer compound, P4N. Although P4N was not visualized unambiguously in the electron density maps, the effect of the drug is evident from significant differences in the lattice constants, crystal packing, and overall conformation of the structure. | |||
Influence of ions, hydration, and the transcriptional inhibitor P4N on the conformations of the Sp1 binding site.,Dohm JA, Hsu MH, Hwu JR, Huang RC, Moudrianakis EN, Lattman EE, Gittis AG J Mol Biol. 2005 Jun 17;349(4):731-44. Epub 2005 Apr 15. PMID:15896803<ref>PMID:15896803</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1zjg" style="background-color:#fffaf0;"></div> | |||
== References == | |||
--> | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
[[Category: Dohm JA]] | |||
[[Category: Gittis AG]] | |||
[[Category: Hsu MH]] | |||
[[Category: Huang RC]] | |||
[[Category: Dohm | [[Category: Hwu JR]] | ||
[[Category: Gittis | [[Category: Lattman EE]] | ||
[[Category: Hsu | [[Category: Moudrianakis EN]] | ||
[[Category: Huang | |||
[[Category: Hwu | |||
[[Category: Lattman | |||
[[Category: Moudrianakis | |||
Latest revision as of 13:31, 16 August 2023
13mer-co13mer-co
Structural highlights
Publication Abstract from PubMedThree crystal structures containing the entire Sp1 consensus sequence d(GGGGCGGGG) with two or three additional base-pairs on either the 5' or 3' ends and overhangs have been determined. Despite the different lengths of DNA in the pseudo-dodecamers and pseudo-tridecamer, all three structures form A-DNA duplexes that share a common set of crystal contacts, including a T*(G.C) base triplet and a 5'-overhang that flips out and away from the helical axes to form a Hoogsteen base-pair with the 3'-overhang of a symmetry mate. The global conformations of the three structures differ, however, in the widths of their respective major grooves, the lengths of the molecules, and the extent of crystal packing. The structures were determined from crystals grown in an unusual precipitant for A-DNA, polyethylene glycol (PEG) 400, in combination with polyamines or ions; cobalt hexamine for the pseudo-tridecamer, and spermidine for the pseudo-dodecamers. As the Sp1 binding site is a target for antiviral and anticancer drugs, pseudo-dodecamer crystals were soaked with one such antiviral and anticancer compound, P4N. Although P4N was not visualized unambiguously in the electron density maps, the effect of the drug is evident from significant differences in the lattice constants, crystal packing, and overall conformation of the structure. Influence of ions, hydration, and the transcriptional inhibitor P4N on the conformations of the Sp1 binding site.,Dohm JA, Hsu MH, Hwu JR, Huang RC, Moudrianakis EN, Lattman EE, Gittis AG J Mol Biol. 2005 Jun 17;349(4):731-44. Epub 2005 Apr 15. PMID:15896803[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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