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.


432d

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:46, 3 April 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:432d.gif|left|200px]]
 
-
<!--
+
==D(GGCCAATTGG) COMPLEXED WITH DAPI==
-
The line below this paragraph, containing "STRUCTURE_432d", creates the "Structure Box" on the page.
+
<StructureSection load='432d' size='340' side='right'caption='[[432d]], [[Resolution|resolution]] 1.89&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[432d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=432D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=432D FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.89&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAP:6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE'>DAP</scene></td></tr>
-
{{STRUCTURE_432d| PDB=432d | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=432d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=432d OCA], [https://pdbe.org/432d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=432d RCSB], [https://www.ebi.ac.uk/pdbsum/432d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=432d ProSAT]</span></td></tr>
-
 
+
</table>
-
'''D(GGCCAATTGG) COMPLEXED WITH DAPI'''
+
__TOC__
-
 
+
</StructureSection>
-
 
+
[[Category: Large Structures]]
-
==Overview==
+
[[Category: Van Meervelt L]]
-
The single-crystal X-ray structure of the complex between the minor groove binder 4',6-diamidino-2-phenylindole (DAPI) and d(GGCCAATTGG) reveals a novel way of off-centered binding, with an unique hydrogen bond between the minor groove binder and a CG base pair. Application of crystal engineering and cryocooling techniques helped to extend the resolution to 1.9 A, resulting in an unambiguous determination of drug conformation and orientation. The structure was refined to completion using SHELXL-93, resulting in a residual factor R of 18. 0% for 3562 reflections with F(o) &gt; 4sigma(F(o)) including 81 water molecules. As the bulky NH(2)-group on guanine is believed to prevent drug binding in the minor groove, the nature and stability of the CG-DAPI contact was further addressed in full detail using ab initio quantum chemical methods. The amino groups involved in the guanine-drug interaction are substantially nonplanar, resulting in an energy gain of about 5 kcal/mol. The combined structural and theoretical data suggest that the guanine NH(2)-group does not destabilize the drug binding to an extent that it prevents complexation.
+
[[Category: Vlieghe D]]
-
 
+
-
==About this Structure==
+
-
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=432D OCA].
+
-
 
+
-
==Reference==
+
-
Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode., Vlieghe D, Sponer J, Van Meervelt L, Biochemistry. 1999 Dec 14;38(50):16443-51. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10600105 10600105]
+
-
[[Category: Meervelt, L Van.]]
+
-
[[Category: Vlieghe, D.]]
+
-
[[Category: 4',6-diamidino-2-phenyl indole]]
+
-
[[Category: Dapi]]
+
-
[[Category: Deoxyribonucleic acid]]
+
-
[[Category: Dna-drug complex]]
+
-
[[Category: Minor groove binder]]
+
-
[[Category: Triplet formation]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:17:32 2008''
+

Current revision

D(GGCCAATTGG) COMPLEXED WITH DAPI

PDB ID 432d

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/432d"
Personal tools