261d

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[[Image:261d.gif|left|200px]]<br /><applet load="261d" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="261d, resolution 2.400&Aring;" />
 
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'''CRYSTAL STRUCTURE OF THE DNA DECAMER D(CGCAATTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF THE DNA DECAMER D(CGCAATTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN==
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The crystal structure of netropsin bound to the decamer d(CGCAATTGCG) has been determined at 2.4 A resolution. This is the first example of a crystal structure of netropsin bound to decamer DNA. The central eight bases of each DNA single-strand base pair with a self-complementary strand to form an octamer B-DNA duplex. These duplexes lie end to end within the unit cell. The terminal 5'-C and G-3' bases are unpaired and interact with the neighboring duplexes via interactions within both the major and minor groove to form base triplet interactions of the type C(+)-G x C and G*(G x C), respectively. The triplet interaction of the type C(+)-G x C is known to exist within triplex DNA with the C+ base oriented parallel with the Watson-Crick guanine base to which it hydrogen bonds. The netropsin molecule lies within the minor groove of the octamer duplex and assumes a class I type position, with bifurcated hydrogen-bonding interactions from the amide groups of the netropsin to the A x T base pairs of the minor groove. The netropsin molecule fits within a five base pair long minor groove site by bending of the flexible amidinium group at one end of the drug.
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<StructureSection load='261d' size='340' side='right'caption='[[261d]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[261d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=261D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=261D FirstGlance]. <br>
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261D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NT:'>NT</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=261D OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<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>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=261d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=261d OCA], [https://pdbe.org/261d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=261d RCSB], [https://www.ebi.ac.uk/pdbsum/261d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=261d ProSAT]</span></td></tr>
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Crystal structure of the DNA decamer d(CGCAATTGCG) complexed with the minor groove binding drug netropsin., Nunn CM, Garman E, Neidle S, Biochemistry. 1997 Apr 22;36(16):4792-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9125500 9125500]
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</table>
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[[Category: Protein complex]]
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__TOC__
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[[Category: Garman, E.]]
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</StructureSection>
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[[Category: Neidle, S.]]
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[[Category: Large Structures]]
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[[Category: Nunn, C M.]]
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[[Category: Garman E]]
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[[Category: NT]]
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[[Category: Neidle S]]
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[[Category: b-dna]]
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[[Category: Nunn CM]]
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[[Category: complexed with drug]]
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[[Category: continuous helix]]
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[[Category: double helix]]
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[[Category: flipped-out bases]]
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[[Category: intermolecular base triplet]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:21:55 2008''
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Current revision

CRYSTAL STRUCTURE OF THE DNA DECAMER D(CGCAATTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN

PDB ID 261d

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