432d
From Proteopedia
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| - | [[Image:432d.gif|left|200px]] | + | [[Image:432d.gif|left|200px]] |
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| - | '''D(GGCCAATTGG) COMPLEXED WITH DAPI''' | + | {{Structure |
| + | |PDB= 432d |SIZE=350|CAPTION= <scene name='initialview01'>432d</scene>, resolution 1.89Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=DAP:6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE'>DAP</scene> | ||
| + | |ACTIVITY= | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''D(GGCCAATTGG) COMPLEXED WITH DAPI''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 432D is a [ | + | 432D 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=432D OCA]. |
==Reference== | ==Reference== | ||
| - | Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode., Vlieghe D, Sponer J, Van Meervelt L, Biochemistry. 1999 Dec 14;38(50):16443-51. PMID:[http:// | + | Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode., Vlieghe D, Sponer J, Van Meervelt L, Biochemistry. 1999 Dec 14;38(50):16443-51. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10600105 10600105] |
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Meervelt, L Van.]] | [[Category: Meervelt, L Van.]] | ||
[[Category: Vlieghe, D.]] | [[Category: Vlieghe, D.]] | ||
[[Category: DAP]] | [[Category: DAP]] | ||
| - | [[Category: | + | [[Category: 4s']] |
[[Category: 6-diamidino-2-phenyl indole]] | [[Category: 6-diamidino-2-phenyl indole]] | ||
[[Category: dapi]] | [[Category: dapi]] | ||
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[[Category: triplet formation]] | [[Category: triplet formation]] | ||
| - | ''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 19:08:14 2008'' |
Revision as of 17:08, 20 March 2008
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| , resolution 1.89Å | |||||||
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| Ligands: | |||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
D(GGCCAATTGG) COMPLEXED WITH DAPI
Overview
The single-crystal X-ray structure of the complex between the minor groove binder 4',6-diamidino-2-phenylindole (DAPI) and d(GGCCAATTGG) reveals a novel way of off-centered binding, with an unique hydrogen bond between the minor groove binder and a CG base pair. Application of crystal engineering and cryocooling techniques helped to extend the resolution to 1.9 A, resulting in an unambiguous determination of drug conformation and orientation. The structure was refined to completion using SHELXL-93, resulting in a residual factor R of 18. 0% for 3562 reflections with F(o) > 4sigma(F(o)) including 81 water molecules. As the bulky NH(2)-group on guanine is believed to prevent drug binding in the minor groove, the nature and stability of the CG-DAPI contact was further addressed in full detail using ab initio quantum chemical methods. The amino groups involved in the guanine-drug interaction are substantially nonplanar, resulting in an energy gain of about 5 kcal/mol. The combined structural and theoretical data suggest that the guanine NH(2)-group does not destabilize the drug binding to an extent that it prevents complexation.
About this Structure
432D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode., Vlieghe D, Sponer J, Van Meervelt L, Biochemistry. 1999 Dec 14;38(50):16443-51. PMID:10600105
Page seeded by OCA on Thu Mar 20 19:08:14 2008
