1cvy

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==CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO CCAGATCTGG==
==CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO CCAGATCTGG==
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<StructureSection load='1cvy' size='340' side='right' caption='[[1cvy]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
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<StructureSection load='1cvy' size='340' side='right'caption='[[1cvy]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[1cvy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CVY FirstGlance]. <br>
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<table><tr><td colspan='2'>[[1cvy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CVY FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPY:IMIDAZOLE-PYRROLE+POLYAMIDE'>IPY</scene><br>
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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]] 2.15&#8491;</td></tr>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1cvx|1cvx]]</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=IPY:IMIDAZOLE-PYRROLE+POLYAMIDE'>IPY</scene></td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1cvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cvy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1cvy RCSB], [http://www.ebi.ac.uk/pdbsum/1cvy PDBsum]</span></td></tr>
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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=1cvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cvy OCA], [https://pdbe.org/1cvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cvy RCSB], [https://www.ebi.ac.uk/pdbsum/1cvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cvy ProSAT]</span></td></tr>
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<table>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Synthetic polyamides composed of three types of aromatic amino acids, N-methylimidazole (Im), N-methylpyrrole (Py) and N-methyl-3-hydroxypyrrole (Hp) bind specific DNA sequences as antiparallel dimers in the minor groove. The side-by-side pairings of aromatic rings in the dimer afford a general recognition code that allows all four base-pairs to be distinguished. To examine the structural consequences of changing the DNA sequence context on T.A recognition by Hp/Py pairs in the minor groove, crystal structures of polyamide dimers (ImPyHpPy)(2) and the pyrrole counterpart (ImPyPyPy)(2) bound to the six base-pair target site 5'-AGATCT-3' in a ten base-pair oligonucleotide have been determined to a resolution of 2.27 and 2.15 A, respectively. The structures demonstrate that the principles of Hp/Py recognition of T.A are consistent between different sequence contexts. However, a general structural explanation for the non-additive reduction in binding affinity due to introduction of the hydroxyl group is less clear. Comparison with other polyamide-DNA cocrystal structures reveals structural themes and differences that may relate to sequence preference.
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Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove.,Kielkopf CL, Bremer RE, White S, Szewczyk JW, Turner JM, Baird EE, Dervan PB, Rees DC J Mol Biol. 2000 Jan 21;295(3):557-67. PMID:10623546<ref>PMID:10623546</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Baird, E. E.]]
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[[Category: Large Structures]]
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[[Category: Bremer, R. E.]]
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[[Category: Baird EE]]
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[[Category: Dervan, P. B.]]
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[[Category: Bremer RE]]
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[[Category: Kielkopf, C. L.]]
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[[Category: Dervan PB]]
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[[Category: Rees, D. C.]]
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[[Category: Kielkopf CL]]
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[[Category: White, S.]]
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[[Category: Rees DC]]
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[[Category: Dna]]
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[[Category: White S]]
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[[Category: Double drug in minor groove]]
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[[Category: Imidazole-pyrrole polyamide]]
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[[Category: Minor groove recognition]]
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Current revision

CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO CCAGATCTGG

PDB ID 1cvy

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