This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


263d

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="263d" size="350" color="white" frame="true" align="right" spinBox="true" caption="263d, resolution 2.200&Aring;" /> '''ISOHELICITY AND PHA...)
Current revision (09:09, 14 February 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:263d.jpg|left|200px]]<br /><applet load="263d" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="263d, resolution 2.200&Aring;" />
 
-
'''ISOHELICITY AND PHASING IN DRUG-DNA SEQUENCE RECOGNITION: CRYSTAL STRUCTURE OF A TRIS(BENZIMIDAZOLE)-OLIGONUCLEOTIDE COMPLEX'''<br />
 
-
==Overview==
+
==ISOHELICITY AND PHASING IN DRUG-DNA SEQUENCE RECOGNITION: CRYSTAL STRUCTURE OF A TRIS(BENZIMIDAZOLE)-OLIGONUCLEOTIDE COMPLEX==
-
The crystal structure is reported of a tris(benzimidazole) analogue of the, minor-groove drug Hoechst 33258 bound to the sequence d(CGCAAATTTGCG)2., The structure has been refined to an R factor of 17.4% at a resolution of, 2.2 A. The ligand covers approximately 7 1/2 base pairs, including the, 5'-AAATTT central sequence. This has an exceptionally narrow minor-groove, width, together with high propeller twists for individual base pairs. The, ligand has a highly twisted structure, with an overall twist of 50 degrees, between aromatic rings. All three benzimidazole subunits are in register, with the DNA, and there is a symmetric group of six hydrogen bonds between, ligand and A.T base-pair edges. By contrast, the ligand does not show an, optimal isohelical fit to the DNA. The correct phasing of drug and DNA, base pairs is ensured by a number of changes to the DNA such that the, central 5'-AAATTT region is slightly unwound relative to the structures of, other noncovalent minor-groove drug complexes.
+
<StructureSection load='263d' size='340' side='right'caption='[[263d]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[263d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=263D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=263D FirstGlance]. <br>
-
263D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=TBZ:'>TBZ</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=263D OCA].
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TBZ:2-(4-METHOXYPHENYL)-5-(3-AMINO-1-PYRROLIDINYL)-2,5,2,5-TRI-BENZIMIDAZOLE'>TBZ</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=263d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=263d OCA], [https://pdbe.org/263d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=263d RCSB], [https://www.ebi.ac.uk/pdbsum/263d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=263d ProSAT]</span></td></tr>
-
Isohelicity and phasing in drug--DNA sequence recognition: crystal structure of a tris(benzimidazole)--oligonucleotide complex., Clark GR, Gray EJ, Neidle S, Li YH, Leupin W, Biochemistry. 1996 Oct 29;35(43):13745-52. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8901516 8901516]
+
</table>
-
[[Category: Protein complex]]
+
__TOC__
-
[[Category: Clark, G.R.]]
+
</StructureSection>
-
[[Category: Gray, E.J.]]
+
[[Category: Large Structures]]
-
[[Category: Leupin, W.]]
+
[[Category: Clark GR]]
-
[[Category: Li, Y.H.]]
+
[[Category: Gray EJ]]
-
[[Category: Neidle, S.]]
+
[[Category: Leupin W]]
-
[[Category: TBZ]]
+
[[Category: Li Y-H]]
-
[[Category: b-dna]]
+
[[Category: Neidle S]]
-
[[Category: complexed with drug]]
+
-
[[Category: double helix]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 17:49:44 2008''
+

Current revision

ISOHELICITY AND PHASING IN DRUG-DNA SEQUENCE RECOGNITION: CRYSTAL STRUCTURE OF A TRIS(BENZIMIDAZOLE)-OLIGONUCLEOTIDE COMPLEX

PDB ID 263d

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/263d"
Personal tools