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.


6bna

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:22, 13 March 2024) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:6bna.jpg|left|200px]]
 
-
{{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 2.210&Aring;
+
<StructureSection load='6bna' size='340' side='right'caption='[[6bna]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <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]] 2.21&#8491;</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>
-
}}
+
<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>
-
 
+
</table>
-
'''BINDING OF AN ANTITUMOR DRUG TO DNA. NETROPSIN AND C-G-C-G-A-A-T-T-BRC-G-C-G'''
+
__TOC__
-
 
+
</StructureSection>
-
 
+
[[Category: Large Structures]]
-
==Overview==
+
[[Category: Dickerson RE]]
-
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: Goodsell D]]
-
 
+
[[Category: Kopka ML]]
-
==About this Structure==
+
[[Category: Pjura P]]
-
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].
+
[[Category: Yoon C]]
-
 
+
-
==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]
+
-
[[Category: Protein complex]]
+
-
[[Category: Dickerson, R E.]]
+
-
[[Category: Goodsell, D.]]
+
-
[[Category: Kopka, M L.]]
+
-
[[Category: Pjura, P.]]
+
-
[[Category: Yoon, C.]]
+
-
[[Category: NT]]
+
-
[[Category: b-dna]]
+
-
[[Category: complexed with drug]]
+
-
[[Category: double helix]]
+
-
[[Category: modified]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 19:13:11 2008''
+

Current revision

BINDING OF AN ANTITUMOR DRUG TO DNA. NETROPSIN AND C-G-C-G-A-A-T-T-BRC-G-C-G

PDB ID 6bna

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/6bna"
Personal tools