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| - | [[Image:1cvy.gif|left|200px]] | |
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| - | {{Structure
| + | ==CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO CCAGATCTGG== |
| - | |PDB= 1cvy |SIZE=350|CAPTION= <scene name='initialview01'>1cvy</scene>, resolution 2.15Å
| + | <StructureSection load='1cvy' size='340' side='right'caption='[[1cvy]], [[Resolution|resolution]] 2.15Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=IPY:IMIDAZOLE-PYRROLE+POLYAMIDE'>IPY</scene>
| + | <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> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.15Å</td></tr> |
| - | |GENE=
| + | <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> |
| - | |DOMAIN=
| + | <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> |
| - | |RELATEDENTRY=[[1cvx|1CVX]]
| + | </table> |
| - | |RESOURCES=<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.ebi.ac.uk/pdbsum/1cvy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1cvy RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO CCAGATCTGG'''
| + | [[Category: Baird EE]] |
| - | | + | [[Category: Bremer RE]] |
| - | | + | [[Category: Dervan PB]] |
| - | ==Overview==
| + | [[Category: Kielkopf CL]] |
| - | 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.
| + | [[Category: Rees DC]] |
| - | | + | [[Category: White S]] |
| - | ==About this Structure==
| + | |
| - | 1CVY is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CVY OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | 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:[http://www.ncbi.nlm.nih.gov/pubmed/10623546 10623546]
| + | |
| - | [[Category: Protein complex]] | + | |
| - | [[Category: Baird, E. E.]] | + | |
| - | [[Category: Bremer, R. E.]] | + | |
| - | [[Category: Dervan, P. B.]] | + | |
| - | [[Category: Kielkopf, C. L.]] | + | |
| - | [[Category: Rees, D. C.]] | + | |
| - | [[Category: White, S.]] | + | |
| - | [[Category: double drug in minor groove]]
| + | |
| - | [[Category: imidazole-pyrrole polyamide]]
| + | |
| - | [[Category: minor groove recognition]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:29:35 2008''
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