459d
From Proteopedia
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|PDB= 459d |SIZE=350|CAPTION= <scene name='initialview01'>459d</scene>, resolution 2.3Å | |PDB= 459d |SIZE=350|CAPTION= <scene name='initialview01'>459d</scene>, resolution 2.3Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=TBZ:2''-(4-METHOXYPHENYL)-5-(3-AMINO-1-PYRROLIDINYL)-2,5',2',5''-TRI-BENZIMIDAZOLE'>TBZ</scene> | + | |LIGAND= <scene name='pdbligand=CBR:5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=TBZ:2''-(4-METHOXYPHENYL)-5-(3-AMINO-1-PYRROLIDINYL)-2,5',2',5''-TRI-BENZIMIDAZOLE'>TBZ</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=459d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=459d OCA], [http://www.ebi.ac.uk/pdbsum/459d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=459d RCSB]</span> | ||
}} | }} | ||
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[[Category: Neidle, S.]] | [[Category: Neidle, S.]] | ||
[[Category: Nunn, C M.]] | [[Category: Nunn, C M.]] | ||
| - | [[Category: TBZ]] | ||
[[Category: b-dna]] | [[Category: b-dna]] | ||
[[Category: complexed with tris-benzimidazole]] | [[Category: complexed with tris-benzimidazole]] | ||
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[[Category: minor groove binding]] | [[Category: minor groove binding]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:37:33 2008'' |
Revision as of 02:37, 31 March 2008
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| , resolution 2.3Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
DNA MINOR-GROOVE RECOGNITION OF A TRIS-BENZIMIDAZOLE DRUG
Overview
The crystal structure of the non-self-complementary dodecamer DNA duplex formed by d(CG[5BrC]ATAT-TTGCG) and d(CGCAAATATGCG) has been solved to 2.3 A resolution, together with that of its complex with the tris-benzimidazole minor groove binding ligand TRIBIZ. The inclusion of a bromine atom on one strand in each structure enabled the possibility of disorder to be discounted. The native structure has an exceptional narrow minor groove, of 2.5-2.6 A in the central part of the A/T region, which is increased in width by approximately 0.8 A on drug binding. The ligand molecule binds in the central part of the sequence. The benzimidazole subunits of the ligand participate in six bifurcated hydrogen bonds with A:T base pair edges, three to each DNA strand. The presence of a pair of C-H...O hydrogen bonds has been deduced from the close proximity of the pyrrolidine group of the ligand to the TpA step in the sequence.
About this Structure
459D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
DNA minor groove recognition of a non-self-complementary AT-rich sequence by a tris-benzimidazole ligand., Aymami J, Nunn CM, Neidle S, Nucleic Acids Res. 1999 Jul 1;27(13):2691-8. PMID:10373586
Page seeded by OCA on Mon Mar 31 05:37:33 2008
