1m6f: Difference between revisions
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[[Image:1m6f.gif|left|200px]] | [[Image:1m6f.gif|left|200px]] | ||
'''Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove''' | {{Structure | ||
|PDB= 1m6f |SIZE=350|CAPTION= <scene name='initialview01'>1m6f</scene>, resolution 1.78Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=CGQ:3-[C-[N'-(3-CARBAMIMIDOYL-BENZYLIDENIUM)-HYDRAZINO]-[[AMINOMETHYLIDENE]AMINIUM]-IMINOMETHYL]-BENZAMIDINIUM'>CGQ</scene> and <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene> | |||
|ACTIVITY= | |||
|GENE= | |||
}} | |||
'''Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1M6F is a [ | 1M6F 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=1M6F OCA]. | ||
==Reference== | ==Reference== | ||
Strong binding in the DNA minor groove by an aromatic diamidine with a shape that does not match the curvature of the groove., Nguyen B, Lee MP, Hamelberg D, Joubert A, Bailly C, Brun R, Neidle S, Wilson WD, J Am Chem Soc. 2002 Nov 20;124(46):13680-1. PMID:[http:// | Strong binding in the DNA minor groove by an aromatic diamidine with a shape that does not match the curvature of the groove., Nguyen B, Lee MP, Hamelberg D, Joubert A, Bailly C, Brun R, Neidle S, Wilson WD, J Am Chem Soc. 2002 Nov 20;124(46):13680-1. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12431090 12431090] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Bailly, C.]] | [[Category: Bailly, C.]] | ||
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[[Category: double helix]] | [[Category: double helix]] | ||
[[Category: minor groove binder]] | [[Category: minor groove binder]] | ||
[[Category: nucleic | [[Category: nucleic acid]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:39:30 2008'' | ||
Revision as of 13:39, 20 March 2008
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| , resolution 1.78Å | |||||||
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| Coordinates: | save as pdb, mmCIF, xml | ||||||
Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove
OverviewOverview
A combination of biophysical techniques has been used to characterize the interaction of an antitrypanosomal agent, CGP 40215A, with DNA. The results from a broad array of methods (DNase I footprinting, surface plasmon resonance, X-ray crystallography, and molecular dynamics) indicate that this compound binds to the minor groove of AT DNA sequences. Despite its unusual linear shape that is not complementary to that of the DNA groove, a high binding affinity was observed in comparison with other similar but more curved diamidine compounds. The amidine groups at both ends of the ligand and the -NH groups on the linker are involved in extensive and dynamic H-bonds to the DNA bases. Complementary and consistent results were obtained from both the X-ray and molecular dynamics studies; both of these methods reveal direct and water-mediated H-bonds between the ligand and the DNA.
About this StructureAbout this Structure
1M6F is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
Strong binding in the DNA minor groove by an aromatic diamidine with a shape that does not match the curvature of the groove., Nguyen B, Lee MP, Hamelberg D, Joubert A, Bailly C, Brun R, Neidle S, Wilson WD, J Am Chem Soc. 2002 Nov 20;124(46):13680-1. PMID:12431090
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