1z8v
From Proteopedia
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|PDB= 1z8v |SIZE=350|CAPTION= <scene name='initialview01'>1z8v</scene>, resolution 1.75Å | |PDB= 1z8v |SIZE=350|CAPTION= <scene name='initialview01'>1z8v</scene>, resolution 1.75Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=NT:NETROPSIN'>NT</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=NT:NETROPSIN'>NT</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1z8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z8v OCA], [http://www.ebi.ac.uk/pdbsum/1z8v PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1z8v RCSB]</span> | ||
}} | }} | ||
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[[Category: Nam, P C.]] | [[Category: Nam, P C.]] | ||
[[Category: Nguyen, M T.]] | [[Category: Nguyen, M T.]] | ||
| - | [[Category: NT]] | ||
[[Category: b-dna double helix]] | [[Category: b-dna double helix]] | ||
[[Category: base triplet]] | [[Category: base triplet]] | ||
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[[Category: netropsin]] | [[Category: netropsin]] | ||
| - | ''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 01:32:14 2008'' |
Revision as of 22:32, 30 March 2008
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| , resolution 1.75Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
The Structure of d(GGCCAATTGG) Complexed with Netropsin
Overview
The structure of the complex between the minor groove binder netropsin and d(GGCCAATTGG) was determined via single-crystal X-ray techniques. The structure was refined to completion using refmac5.1.24, resulting in a residual R-factor of 20.0% (including 68 water molecules). Using crystal engineering and cryocooling techniques, the resolution could be enhanced to 1.75 A, resulting in an unambiguous determination of the drug conformation and orientation. As previously noticed, bifurcated hydrogen bonds are formed between the amide nitrogen atoms of the drug and the N3 and O2 atoms of A and T base pairs, respectively, clearly cataloging the structure to class I. As the bulky NH2 group on guanine was believed to prevent binding of the drug in the minor groove, the detailed nature of several of the amidinium and guanidinium end contacts were further investigated by ab initio quantum chemical methods.
About this Structure
1Z8V is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Netropsin interactions in the minor groove of d(GGCCAATTGG) studied by a combination of resolution enhancement and ab initio calculations., Van Hecke K, Nam PC, Nguyen MT, Van Meervelt L, FEBS J. 2005 Jul;272(14):3531-41. PMID:16008554
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