6bna: Difference between revisions

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<StructureSection load='6bna' size='340' side='right'caption='[[6bna]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
<StructureSection load='6bna' size='340' side='right'caption='[[6bna]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6bna]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BNA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6BNA FirstGlance]. <br>
<table><tr><td colspan='2'>[[6bna]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BNA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BNA FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NT:NETROPSIN'>NT</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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=NT:NETROPSIN'>NT</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6bna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bna OCA], [http://pdbe.org/6bna PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bna RCSB], [http://www.ebi.ac.uk/pdbsum/6bna PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bna 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=6bna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bna OCA], [https://pdbe.org/6bna PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bna RCSB], [https://www.ebi.ac.uk/pdbsum/6bna PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bna ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The antitumor antibiotic netropsin has been co-crystallized with a double-helical B-DNA dodecanucleotide of sequence: C-G-C-G-A-A-T-T-BrC-G-C-G, and the structure of the complex has been solved by X-ray diffraction at a resolution of 2.2 A. The structure has been refined independently by Jack-Levitt and Hendrickson-Konnert least-squares methods, leading to a final residual error of 0.257 by the Jack-Levitt approach (0.211 for two-sigma data) or 0.248 by the Hendrickson-Konnert approach, with no significant difference between refined structures. The netropsin molecule displaces the spine of hydration and fits snugly within the minor groove in the A-A-T-T center. It widens the groove slightly and bends the helix axis back by 8 degrees, but neither unwinds nor elongates the double helix. The drug molecule is held in place by amide NH hydrogen bonds that bridge adenine N-3 and thymine O-2 atoms, exactly as with the spine of hydration. The requirement of A X T base-pairs in the binding site arises because the N-2 amino group of guanine would demand impermissibly close contacts with netropsin. It is proposed that substitution of imidazole for pyrrole in netropsin should create a family of "lexitropsins" capable of reading G X C-containing base sequences.
Binding of an antitumor drug to DNA, Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G.,Kopka ML, Yoon C, Goodsell D, Pjura P, Dickerson RE J Mol Biol. 1985 Jun 25;183(4):553-63. PMID:2991536<ref>PMID:2991536</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6bna" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Dickerson, R E]]
[[Category: Dickerson RE]]
[[Category: Goodsell, D]]
[[Category: Goodsell D]]
[[Category: Kopka, M L]]
[[Category: Kopka ML]]
[[Category: Pjura, P]]
[[Category: Pjura P]]
[[Category: Yoon, C]]
[[Category: Yoon C]]
[[Category: B-dna]]
[[Category: Complexed with drug]]
[[Category: Dna]]
[[Category: Double helix]]
[[Category: Modified]]

Latest revision as of 14:22, 13 March 2024

BINDING OF AN ANTITUMOR DRUG TO DNA. NETROPSIN AND C-G-C-G-A-A-T-T-BRC-G-C-G

6bna, resolution 2.21Å

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