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| - | [[Image:2dbe.jpg|left|200px]] | |
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| - | {{Structure
| + | ==CRYSTAL STRUCTURE OF A BERENIL-DODECANUCLEOTIDE COMPLEX: THE ROLE OF WATER IN SEQUENCE-SPECIFIC LIGAND BINDING== |
| - | |PDB= 2dbe |SIZE=350|CAPTION= <scene name='initialview01'>2dbe</scene>, resolution 2.500Å
| + | <StructureSection load='2dbe' size='340' side='right'caption='[[2dbe]], [[Resolution|resolution]] 2.50Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=BRN:BERENIL'>BRN</scene>, <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>
| + | <table><tr><td colspan='2'>[[2dbe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DBE 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]] 2.5Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRN:BERENIL'>BRN</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=2dbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dbe OCA], [https://pdbe.org/2dbe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dbe RCSB], [https://www.ebi.ac.uk/pdbsum/2dbe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dbe ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dbe OCA], [http://www.ebi.ac.uk/pdbsum/2dbe PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dbe RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''CRYSTAL STRUCTURE OF A BERENIL-DODECANUCLEOTIDE COMPLEX: THE ROLE OF WATER IN SEQUENCE-SPECIFIC LIGAND BINDING'''
| + | [[Category: Brown DG]] |
| - | | + | [[Category: Brown T]] |
| - | | + | [[Category: Garman E]] |
| - | ==Overview==
| + | [[Category: Jenkins TC]] |
| - | The three-dimensional structure of a complex between the dodecanucleotide d(CGCGAATTCGCG) and the anti-trypanocidal drug berenil, has been determined to a resolution of 2.5 A. The structure has been solved by molecular replacement and refined to an R factor of 0.177. A total of 49 water molecules have been located. The drug is bound at the 5'-AAT-3' region of the oligonucleotide. At one end of the drug the amidinium group is in hydrogen-bonded contact with N3 of the adenine base complementary to the thymine of the AAT. The other amidinium group does not make direct interactions with the DNA. Instead, a water molecule mediates between them. This is in hydrogen-bonded contact with an amidinium nitrogen atom, N3 of the 5' end adenine base and the ring oxygen atom of an adjacent deoxyribose. Molecular mechanics calculations have been performed on this complex, with the drug at various positions along the sequence. These show that the observed position is only 0.8 kcal/mol higher in energy than the best position. It is suggested that there is a broad energy well in the AATT region for this drug, and that water molecules as well as the neighbouring sequence, will determine precise positioning. More general aspects of minor groove binding are discussed.
| + | [[Category: Neidle S]] |
| - | | + | [[Category: Sanderson MR]] |
| - | ==About this Structure==
| + | [[Category: Skelly JV]] |
| - | 2DBE 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=2DBE OCA].
| + | [[Category: Stuart DI]] |
| - | | + | |
| - | ==Reference==
| + | |
| - | Crystal structure of a berenil-dodecanucleotide complex: the role of water in sequence-specific ligand binding., Brown DG, Sanderson MR, Skelly JV, Jenkins TC, Brown T, Garman E, Stuart DI, Neidle S, EMBO J. 1990 Apr;9(4):1329-34. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2323343 2323343]
| + | |
| - | [[Category: Protein complex]] | + | |
| - | [[Category: Brown, D G.]] | + | |
| - | [[Category: Brown, T.]] | + | |
| - | [[Category: Garman, E.]] | + | |
| - | [[Category: Jenkins, T C.]] | + | |
| - | [[Category: Neidle, S.]] | + | |
| - | [[Category: Sanderson, M R.]] | + | |
| - | [[Category: Skelly, J V.]] | + | |
| - | [[Category: Stuart, D I.]] | + | |
| - | [[Category: b-dna]]
| + | |
| - | [[Category: complexed with drug]]
| + | |
| - | [[Category: double helix]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:32:28 2008''
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