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.


1z8v

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:02, 14 February 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1z8v.gif|left|200px]]
 
-
<!--
+
==The Structure of d(GGCCAATTGG) Complexed with Netropsin==
-
The line below this paragraph, containing "STRUCTURE_1z8v", creates the "Structure Box" on the page.
+
<StructureSection load='1z8v' size='340' side='right'caption='[[1z8v]], [[Resolution|resolution]] 1.75&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'>[[1z8v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z8V 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]] 1.75&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NT:NETROPSIN'>NT</scene></td></tr>
-
{{STRUCTURE_1z8v| PDB=1z8v | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1z8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z8v OCA], [https://pdbe.org/1z8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z8v RCSB], [https://www.ebi.ac.uk/pdbsum/1z8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z8v ProSAT]</span></td></tr>
-
 
+
</table>
-
'''The Structure of d(GGCCAATTGG) Complexed with Netropsin'''
+
__TOC__
-
 
+
</StructureSection>
-
 
+
[[Category: Large Structures]]
-
==Overview==
+
[[Category: Nam PC]]
-
The structure of the complex between the minor groove binder netropsin and d(GGCCAATTGG) was determined via single-crystal X-ray techniques. The structure was refined to completion using refmac5.1.24, resulting in a residual R-factor of 20.0% (including 68 water molecules). Using crystal engineering and cryocooling techniques, the resolution could be enhanced to 1.75 A, resulting in an unambiguous determination of the drug conformation and orientation. As previously noticed, bifurcated hydrogen bonds are formed between the amide nitrogen atoms of the drug and the N3 and O2 atoms of A and T base pairs, respectively, clearly cataloging the structure to class I. As the bulky NH2 group on guanine was believed to prevent binding of the drug in the minor groove, the detailed nature of several of the amidinium and guanidinium end contacts were further investigated by ab initio quantum chemical methods.
+
[[Category: Nguyen MT]]
-
 
+
[[Category: Van Hecke K]]
-
==About this Structure==
+
[[Category: Van Meervelt L]]
-
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z8V OCA].
+
-
 
+
-
==Reference==
+
-
Netropsin interactions in the minor groove of d(GGCCAATTGG) studied by a combination of resolution enhancement and ab initio calculations., Van Hecke K, Nam PC, Nguyen MT, Van Meervelt L, FEBS J. 2005 Jul;272(14):3531-41. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16008554 16008554]
+
-
[[Category: Hecke, K Van.]]
+
-
[[Category: Meervelt, L Van.]]
+
-
[[Category: Nam, P C.]]
+
-
[[Category: Nguyen, M T.]]
+
-
[[Category: B-dna double helix]]
+
-
[[Category: Base triplet]]
+
-
[[Category: Drug]]
+
-
[[Category: Minor groove binder]]
+
-
[[Category: Netropsin]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 17:19:28 2008''
+

Current revision

The Structure of d(GGCCAATTGG) Complexed with Netropsin

PDB ID 1z8v

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/1z8v"
Personal tools