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[[Image:121d.jpg|left|200px]]


{{Structure
==MOLECULAR STRUCTURE OF THE A-TRACT DNA DODECAMER D(CGCAAATTTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN==
|PDB= 121d |SIZE=350|CAPTION= <scene name='initialview01'>121d</scene>, resolution 2.200&Aring;
<StructureSection load='121d' size='340' side='right'caption='[[121d]], [[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=NT:NETROPSIN'>NT</scene>
<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>
|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=NT:NETROPSIN'>NT</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=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>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=121d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=121d OCA], [http://www.ebi.ac.uk/pdbsum/121d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=121d RCSB]</span>
__TOC__
}}
</StructureSection>
 
[[Category: Large Structures]]
'''MOLECULAR STRUCTURE OF THE A-TRACT DNA DODECAMER D(CGCAAATTTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN'''
[[Category: Aymami J]]
 
[[Category: Coll M]]
 
[[Category: Fita I]]
==Overview==
[[Category: Rich A]]
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: Tabernero L]]
 
[[Category: Van Boom JH]]
==About this Structure==
[[Category: Van Der Marel GA]]
121D 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=121D OCA].
[[Category: Verdaguer N]]
 
==Reference==
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: Protein complex]]
[[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 Sun Mar 30 18:27:09 2008''

Latest revision as of 09:24, 7 February 2024

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

Structural highlights

121d is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

121d, resolution 2.20Å

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