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| - | [[Image:305d.jpg|left|200px]] | |
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| - | {{Structure
| + | ==SIDE-BY-SIDE BINDING OF DISTAMYCIN MOLECULES TO D(ICATATIC) IN THE TETRAGONAL FORM== |
| - | |PDB= 305d |SIZE=350|CAPTION= <scene name='initialview01'>305d</scene>, resolution 2.170Å
| + | <StructureSection load='305d' size='340' side='right'caption='[[305d]], [[Resolution|resolution]] 2.17Å' 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=DI:2'-DEOXYINOSINE-5'-MONOPHOSPHATE'>DI</scene>, <scene name='pdbligand=DMY:DISTAMYCIN+A'>DMY</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
| + | <table><tr><td colspan='2'>[[305d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=305D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=305D 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]] 2.17Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMY:DISTAMYCIN+A'>DMY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=305d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=305d OCA], [https://pdbe.org/305d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=305d RCSB], [https://www.ebi.ac.uk/pdbsum/305d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=305d ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=305d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=305d OCA], [http://www.ebi.ac.uk/pdbsum/305d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=305d RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''SIDE-BY-SIDE BINDING OF DISTAMYCIN MOLECULES TO D(ICATATIC) IN THE TETRAGONAL FORM'''
| + | [[Category: Chen X]] |
| - | | + | [[Category: Ramakrishnan B]] |
| - | | + | [[Category: Sundaralingam M]] |
| - | ==Overview==
| + | |
| - | To understand the recognition interactions between AT-containing alternating DNA and minor groove binding drugs, the crystal structures of the side-by-side binding of two distamycin molecules to the DNA octamers d(ICITACIC)2 and d(ICATATIC)2, referred to here as TA and ATAT, respectively, have been determined at 1.6 A and 2.2 A, respectively. Compared to the previous 2:1 all-IC d(ICICICIC)2-distamycin complex, the substitutions of the I x C base-pairs by the A x T base-pairs enable the interactions of the drug with its natural target to be studied. Both complexes assume side-by-side drug binding, isomorphous to the all IC counterpart in the tetragonal space group P4(1)22 (a = b = 28.03 A, c = 58.04 A and a = b = 27.86 A, c = 58.62 A, respectively). The ATAT complex also crystallized in a new polymorphic monoclinic space group C2 (a = 33.38 A, b = 25.33 A, c = 28.11 A and beta = 120.45 degrees) and was solved at 1.9 A resolution. The structures of the three double drug x DNA complexes are very similar, characterized by systematic hydrogen bonding and van der Waals interactions. Each drug hydrogen bonds with the bases of the proximal DNA strand only and stacks with the sugar moiety, while the side-by-side drugs themselves exhibit pyrrole ring-peptide stacking. The pyrrole-peptide interaction is crucial for the side-by-side binding mode of the distamycin/netropsin family of drugs. The purine-pyrimidine alternation is probably responsible for the striking alternation in the helical and backbone conformations. The structures are conserved between the pure IC complex and the AT substituted complexes but further details of the side-by-side binding to DNA are provided by the 1.6 A resolution structure of TA.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 305D 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=305D OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Crystal structures of the side-by-side binding of distamycin to AT-containing DNA octamers d(ICITACIC) and d(ICATATIC)., Chen X, Ramakrishnan B, Sundaralingam M, J Mol Biol. 1997 Apr 18;267(5):1157-70. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9150404 9150404]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Chen, X.]] | + | |
| - | [[Category: Ramakrishnan, B.]] | + | |
| - | [[Category: Sundaralingam, M.]] | + | |
| - | [[Category: b-dna]]
| + | |
| - | [[Category: complexed with drug]]
| + | |
| - | [[Category: double drug in the minor groove]]
| + | |
| - | [[Category: double helix]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:21:06 2008''
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