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.


166d

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:25, 7 February 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:166d.jpg|left|200px]]
 
-
{{Structure
+
==DRUG-DNA MINOR GROOVE RECOGNITION: CRYSTAL STRUCTURE OF GAMMA-OXAPENTAMIDINE COMPLEXED WITH D(CGCGAATTCGCG)2==
-
|PDB= 166d |SIZE=350|CAPTION= <scene name='initialview01'>166d</scene>, resolution 2.200&Aring;
+
<StructureSection load='166d' size='340' side='right'caption='[[166d]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=PET:1,5-DI(4-AMIDINOPHENOXY)-3-OXA-PENTANE'>PET</scene>
+
<table><tr><td colspan='2'>[[166d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=166D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=166D 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]] 2.2&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PET:1,5-DI(4-AMIDINOPHENOXY)-3-OXA-PENTANE'>PET</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=166d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=166d OCA], [https://pdbe.org/166d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=166d RCSB], [https://www.ebi.ac.uk/pdbsum/166d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=166d ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=166d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=166d OCA], [http://www.ebi.ac.uk/pdbsum/166d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=166d RCSB]</span>
+
__TOC__
-
}}
+
</StructureSection>
-
 
+
[[Category: Large Structures]]
-
'''DRUG-DNA MINOR GROOVE RECOGNITION: CRYSTAL STRUCTURE OF GAMMA-OXAPENTAMIDINE COMPLEXED WITH D(CGCGAATTCGCG)2'''
+
[[Category: Jenkins TC]]
-
 
+
[[Category: Neidle S]]
-
 
+
[[Category: Nunn CM]]
-
==Overview==
+
-
The crystal structure of the complex of gamma-oxapentamidine and the DNA dodecamer d(CGCGAATTCGCG)2 has been determined to a resolution of 0.22 nm and an R factor of 18.9%. The gamma-oxapentamidine ligand interacts with the dodecamer by classic minor groove binding via interactions within the A+T-rich region of the minor groove. A chain of solvent molecules lies along the mouth of the minor groove on the outside of the bound ligand. The structural details of the complex are discussed and compared with the closely analogous complex with pentamidine bound to the same dodecamer [Edwards, K. J., Jenkins, T. C. &amp; Neidle, S. (1992) Biochemistry 31, 7104-7109]. The amidinium groups of the ligand do not hydrogen bond to bases, but are in close contact with O4' sugar ring atoms. This in part explains the reduced DNA binding affinity of this ligand compared to pentamidine.
+
-
 
+
-
==About this Structure==
+
-
166D 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=166D OCA].
+
-
 
+
-
==Reference==
+
-
Crystal structure of gamma-oxapentamidine complexed with d(CGCGAATTCGCG)2. The effects of drug structural change on DNA minor-groove recognition., Nunn CM, Jenkins TC, Neidle S, Eur J Biochem. 1994 Dec 15;226(3):953-61. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7813486 7813486]
+
-
[[Category: Protein complex]]
+
-
[[Category: Jenkins, T C.]]
+
-
[[Category: Neidle, S.]]
+
-
[[Category: Nunn, C M.]]
+
-
[[Category: b-dna]]
+
-
[[Category: complexed with drug]]
+
-
[[Category: double helix]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:28:50 2008''
+

Current revision

DRUG-DNA MINOR GROOVE RECOGNITION: CRYSTAL STRUCTURE OF GAMMA-OXAPENTAMIDINE COMPLEXED WITH D(CGCGAATTCGCG)2

PDB ID 166d

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/166d"
Personal tools