166d
From Proteopedia
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|PDB= 166d |SIZE=350|CAPTION= <scene name='initialview01'>166d</scene>, resolution 2.200Å | |PDB= 166d |SIZE=350|CAPTION= <scene name='initialview01'>166d</scene>, resolution 2.200Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=PET:1,5-DI(4-AMIDINOPHENOXY)-3-OXA-PENTANE'>PET</scene> | + | |LIGAND= <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=PET:1,5-DI(4-AMIDINOPHENOXY)-3-OXA-PENTANE'>PET</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |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> | ||
}} | }} | ||
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[[Category: Neidle, S.]] | [[Category: Neidle, S.]] | ||
[[Category: Nunn, C M.]] | [[Category: Nunn, C M.]] | ||
| - | [[Category: PET]] | ||
[[Category: b-dna]] | [[Category: b-dna]] | ||
[[Category: complexed with drug]] | [[Category: complexed with drug]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:28:50 2008'' |
Revision as of 15:28, 30 March 2008
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| , resolution 2.200Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
DRUG-DNA MINOR GROOVE RECOGNITION: CRYSTAL STRUCTURE OF GAMMA-OXAPENTAMIDINE COMPLEXED WITH D(CGCGAATTCGCG)2
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. & 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 [1]. Full crystallographic information is available from 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:7813486
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