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| - | [[Image:6bna.jpg|left|200px]] | |
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| - | {{Structure
| + | ==BINDING OF AN ANTITUMOR DRUG TO DNA. NETROPSIN AND C-G-C-G-A-A-T-T-BRC-G-C-G== |
| - | |PDB= 6bna |SIZE=350|CAPTION= <scene name='initialview01'>6bna</scene>, resolution 2.210Å
| + | <StructureSection load='6bna' size='340' side='right'caption='[[6bna]], [[Resolution|resolution]] 2.21Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=CBR:5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE'>CBR</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>, <scene name='pdbligand=NT:NETROPSIN'>NT</scene>
| + | <table><tr><td colspan='2'>[[6bna]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BNA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BNA 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]] 2.21Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=NT:NETROPSIN'>NT</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=6bna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bna OCA], [https://pdbe.org/6bna PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bna RCSB], [https://www.ebi.ac.uk/pdbsum/6bna PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bna ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6bna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bna OCA], [http://www.ebi.ac.uk/pdbsum/6bna PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=6bna RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''BINDING OF AN ANTITUMOR DRUG TO DNA. NETROPSIN AND C-G-C-G-A-A-T-T-BRC-G-C-G'''
| + | [[Category: Dickerson RE]] |
| - | | + | [[Category: Goodsell D]] |
| - | | + | [[Category: Kopka ML]] |
| - | ==Overview==
| + | [[Category: Pjura P]] |
| - | The antitumor antibiotic netropsin has been co-crystallized with a double-helical B-DNA dodecanucleotide of sequence: C-G-C-G-A-A-T-T-BrC-G-C-G, and the structure of the complex has been solved by X-ray diffraction at a resolution of 2.2 A. The structure has been refined independently by Jack-Levitt and Hendrickson-Konnert least-squares methods, leading to a final residual error of 0.257 by the Jack-Levitt approach (0.211 for two-sigma data) or 0.248 by the Hendrickson-Konnert approach, with no significant difference between refined structures. The netropsin molecule displaces the spine of hydration and fits snugly within the minor groove in the A-A-T-T center. It widens the groove slightly and bends the helix axis back by 8 degrees, but neither unwinds nor elongates the double helix. The drug molecule is held in place by amide NH hydrogen bonds that bridge adenine N-3 and thymine O-2 atoms, exactly as with the spine of hydration. The requirement of A X T base-pairs in the binding site arises because the N-2 amino group of guanine would demand impermissibly close contacts with netropsin. It is proposed that substitution of imidazole for pyrrole in netropsin should create a family of "lexitropsins" capable of reading G X C-containing base sequences.
| + | [[Category: Yoon C]] |
| - | | + | |
| - | ==About this Structure==
| + | |
| - | 6BNA 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=6BNA OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Binding of an antitumor drug to DNA, Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G., Kopka ML, Yoon C, Goodsell D, Pjura P, Dickerson RE, J Mol Biol. 1985 Jun 25;183(4):553-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2991536 2991536]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Dickerson, R E.]] | + | |
| - | [[Category: Goodsell, D.]] | + | |
| - | [[Category: Kopka, M L.]] | + | |
| - | [[Category: Pjura, P.]] | + | |
| - | [[Category: Yoon, C.]] | + | |
| - | [[Category: b-dna]]
| + | |
| - | [[Category: complexed with drug]]
| + | |
| - | [[Category: double helix]]
| + | |
| - | [[Category: modified]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:42:40 2008''
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