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| - | [[Image:102d.gif|left|200px]] | |
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| - | {{Structure
| + | ==SEQUENCE-DEPENDENT DRUG BINDING TO THE MINOR GROOVE OF DNA: THE CRYSTAL STRUCTURE OF THE DNA DODECAMER D(CGCAAATTTGCG)2 COMPLEXED WITH PROPAMIDINE== |
| - | |PDB= 102d |SIZE=350|CAPTION= <scene name='initialview01'>102d</scene>, resolution 2.200Å
| + | <StructureSection load='102d' size='340' side='right'caption='[[102d]], [[Resolution|resolution]] 2.20Å' 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=TNT:1,3-BIS(AMIDINOPHENOXY)PROPANE'>TNT</scene>
| + | <table><tr><td colspan='2'>[[102d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=102D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=102D 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]] 2.2Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TNT:1,3-BIS(AMIDINOPHENOXY)PROPANE'>TNT</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=102d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=102d OCA], [https://pdbe.org/102d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=102d RCSB], [https://www.ebi.ac.uk/pdbsum/102d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=102d ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=102d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=102d OCA], [http://www.ebi.ac.uk/pdbsum/102d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=102d RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''SEQUENCE-DEPENDENT DRUG BINDING TO THE MINOR GROOVE OF DNA: THE CRYSTAL STRUCTURE OF THE DNA DODECAMER D(CGCAAATTTGCG)2 COMPLEXED WITH PROPAMIDINE'''
| + | [[Category: Neidle S]] |
| - | | + | [[Category: Nunn CM]] |
| - | | + | |
| - | ==Overview==
| + | |
| - | The DNA-binding ligand propamidine, an analogue of the drug pentamidine which is used in the treatment of acquired immune deficiency syndrome (AIDS)-associated Pneumocystis carinii, has been cocrystallized with the DNA sequence d(CGCAAATTTGCG)2, and the crystal structure of the complex has been determined using data from 8 to 2.2 A resolution. The R factor converged to 15.5% with the inclusion of 73 water molecules. The structure shows binding of the propamidine molecule within the AT tract of the DNA minor groove with a shift from the center of the duplex toward the 3' end of ca. 2 A. The long AT tract of six base pairs in length allows the propamidine many potential binding sites in the DNA groove, and its binding is seen to occur where there is least perturbation to the DNA from that seen in the native structure. The interactions with bases are distinct from those previously observed for the sequence d(CGCGAATTCGCG)2.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 102D 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=102D OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Sequence-dependent drug binding to the minor groove of DNA: crystal structure of the DNA dodecamer d(CGCAAATTTGCG)2 complexed with propamidine., Nunn CM, Neidle S, J Med Chem. 1995 Jun 23;38(13):2317-25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7608897 7608897]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Neidle, S.]] | + | |
| - | [[Category: Nunn, C M.]] | + | |
| - | [[Category: b-dna]]
| + | |
| - | [[Category: complexed with drug]]
| + | |
| - | [[Category: double helix]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:26:17 2008''
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