1ovf: Difference between revisions

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-[[Image:1ovf.png|left|200px]]
-<!--
+==NMR Structure of ActD/5'-CCGTTTTGTGG-3' Complex==
-The line below this paragraph, containing "STRUCTURE_1ovf", creates the "Structure Box" on the page.
+<StructureSection load='1ovf' size='340' side='right'caption='[[1ovf]]' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1ovf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_antibioticus Streptomyces antibioticus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OVF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OVF FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 10 models</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DVA:D-VALINE'>DVA</scene>, <scene name='pdbligand=MVA:N-METHYLVALINE'>MVA</scene>, <scene name='pdbligand=PXZ:2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE'>PXZ</scene>, <scene name='pdbligand=SAR:SARCOSINE'>SAR</scene></td></tr>
-{{STRUCTURE_1ovf|  PDB=1ovf  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ovf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ovf OCA], [https://pdbe.org/1ovf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ovf RCSB], [https://www.ebi.ac.uk/pdbsum/1ovf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ovf ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Binding of actinomycin D (ActD) to the seemingly single-stranded DNA (ssDNA) oligomer 5'-CCGTT3 GTGG-3' has been studied in solution using high-resolution nuclear magnetic resonance (NMR) techniques. A strong binding constant (8 x 10(6) M(-1)) and high quality NMR spectra have allowed us to determine the initial DNA structure using distance geometry as well as the final ActD-5'-CCGTT3 GTGG-3' complex structure using constrained molecular dynamics calculations. The DNA oligomer 5'-CCGTT3GTGG-3' in the complex forms a hairpin structure with tandem G.T mismatches at the stem region next to a loop of three stacked thymine bases pointing toward the major groove. Bipartite T2O-GH1 and T2O-G2NH2 hydrogen bonds were detected for the G.T mismatches that further stabilize this unusual DNA hairpin. The phenoxazone chromophore of ActD intercalates nicely between the tandem G.T mismatches in essentially one major orientation. Additional hydrophobic interactions between the ActD quinoid amino acid residues with the loop T5-T6-T7 backbone protons were also observed. The hydrophobic G-phenoxazone-G interaction in the ActD-5'-CCGTT3GTGG-3' complex is more robust than that of the classical ActD- 5'-CCGCT3GCGG-3' complex, consistent with the roughly 2-fold stronger binding of ActD to the 5'-CCGTT3GTGG-3' sequence than to its 5'-CCG CT3GCGG-3' counterpart. Stabilization by ActD of a hairpin containing non-canonical stem base pairs further strengthens the notion that ActD or other related compounds may serve as a sequence- specific ssDNA-binding agent that inhibits human immunodeficiency virus (HIV) and other retroviruses replicating through ssDNA intermediates.
-===NMR Structure of ActD/5'-CCGTTTTGTGG-3' Complex===
+Solution structure of the ActD-5'-CCGTT3GTGG-3' complex: drug interaction with tandem G.T mismatches and hairpin loop backbone.,Chin KH, Chen FM, Chou SH Nucleic Acids Res. 2003 May 15;31(10):2622-9. PMID:12736312<ref>PMID:12736312</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_12736312}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1ovf" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 12736312 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12736312}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[1ovf]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OVF OCA].
+[[Category: Streptomyces antibioticus]]
+[[Category: Chen F-M]]
-==Reference==
+[[Category: Chin K-H]]
-<ref group="xtra">PMID:012736312</ref><references group="xtra"/>
+[[Category: Chou S-H]]
-[[Category: Chen, F M.]]
-[[Category: Chin, K H.]]
-[[Category: Chou, S H.]]
-[[Category: Actinomycin]]
-[[Category: Actinomycin d]]
-[[Category: Anti cancer]]
-[[Category: Antibiotic]]
-[[Category: Antitumor]]
-[[Category: Chromophore]]
-[[Category: Depsipeptide]]
-[[Category: Dna-antibiotic complex]]
-[[Category: Mismatch]]