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.


121d

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:24, 7 February 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:121d.jpg|left|200px]]
 
-
<!--
+
==MOLECULAR STRUCTURE OF THE A-TRACT DNA DODECAMER D(CGCAAATTTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN==
-
The line below this paragraph, containing "STRUCTURE_121d", creates the "Structure Box" on the page.
+
<StructureSection load='121d' size='340' side='right'caption='[[121d]], [[Resolution|resolution]] 2.20&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'>[[121d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=121D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=121D 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]] 2.2&#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_121d| PDB=121d | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=121d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=121d OCA], [https://pdbe.org/121d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=121d RCSB], [https://www.ebi.ac.uk/pdbsum/121d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=121d ProSAT]</span></td></tr>
-
 
+
</table>
-
'''MOLECULAR STRUCTURE OF THE A-TRACT DNA DODECAMER D(CGCAAATTTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN'''
+
__TOC__
-
 
+
</StructureSection>
-
 
+
[[Category: Large Structures]]
-
==Overview==
+
[[Category: Aymami J]]
-
The molecular structure of the complex between the minor groove binding drug netropsin and the dodecamer d(CGCAAATTTGCG) has been solved and refined by X-ray diffraction analysis to an R-factor of 19.8% and 2.2-A resolution. The drug lies in the narrow minor groove of the B-DNA fragment, covering five of the six A.T base pairs (from A5.T20 to T9.A16). The long six A.T base pair tract allows the drug to bind in a position that optimizes its contacts with the DNA, establishing hydrogen bonds with O2 of thymines and N3 of adenines. The DNA molecule shows a high propeller twist only at the A6.T19 step of the A-tract. Two three-centered hydrogen bonds are observed in the major groove at half of the A-tract.
+
[[Category: Coll M]]
-
 
+
[[Category: Fita I]]
-
==About this Structure==
+
[[Category: Rich A]]
-
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=121D OCA].
+
[[Category: Tabernero L]]
-
 
+
[[Category: Van Boom JH]]
-
==Reference==
+
[[Category: Van Der Marel GA]]
-
Molecular structure of the A-tract DNA dodecamer d(CGCAAATTTGCG) complexed with the minor groove binding drug netropsin., Tabernero L, Verdaguer N, Coll M, Fita I, van der Marel GA, van Boom JH, Rich A, Aymami J, Biochemistry. 1993 Aug 24;32(33):8403-10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8395202 8395202]
+
[[Category: Verdaguer N]]
-
[[Category: Aymami, J.]]
+
-
[[Category: Boom, J H.Van.]]
+
-
[[Category: Coll, M.]]
+
-
[[Category: Fita, I.]]
+
-
[[Category: Marel, G A.Van Der.]]
+
-
[[Category: Rich, A.]]
+
-
[[Category: Tabernero, L.]]
+
-
[[Category: Verdaguer, N.]]
+
-
[[Category: B-dna]]
+
-
[[Category: Complexed with drug]]
+
-
[[Category: Double helix]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 09:27:42 2008''
+

Current revision

MOLECULAR STRUCTURE OF THE A-TRACT DNA DODECAMER D(CGCAAATTTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN

PDB ID 121d

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/121d"
Personal tools