1dvl: Difference between revisions

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[[Image:1dvl.gif|left|200px]]
{{Seed}}
[[Image:1dvl.png|left|200px]]


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{{STRUCTURE_1dvl|  PDB=1dvl  |  SCENE=  }}  
{{STRUCTURE_1dvl|  PDB=1dvl  |  SCENE=  }}  


'''CRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COMPLEX WITH ONLY ONE DRUG BOUND AT ONE END'''
===CRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COMPLEX WITH ONLY ONE DRUG BOUND AT ONE END===




==Overview==
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The crystal structure of the 1:1 complex of netropsin and the B-DNA decamer d(CCIICICCII)(2) has been elucidated and refined to an R factor of 19.6% and an R(free) of 24.7% using 1790 reflections in the resolution range 8-2.4 A. The complex crystallizes in space group C2, with unit-cell parameters a = 62.40, b = 24.47, c = 36.31 A, beta = 110.09 degrees and one molecule of netropsin in the asymmetric unit; the rest of the minor groove is filled with six water molecules. The structure was solved by the molecular-replacement method using the DNA model d(CCCCCIIIII)(2) from the 2:1 netropsin complex by removing both bound netropsins (Chen et al., 1998). Surprisingly, only one netropsin molecule is found to bind to the present decamer, covering residues 2-6 at the upper stream of the duplex. The positively charged guanidinium head is hydrogen bonded through N1H(2) to the O(2) of cytosine 2 and through N10H(2) to N(3) of inosine 6. The three amide N-H groups of the peptides face the minor groove and form three sets of bifurcated hydrogen bonds with the base atoms. The central part of the drug (C3-N8) is nearly conjugated. The preference of the cytosine carbonyl O2 atoms over the inosine N3 atoms in hydrogen bonding is seen. The drug-bound region has more uniform twists, roll angles, propeller twists and minor-groove widths compared with the water-bound region.
The line below this paragraph, {{ABSTRACT_PUBMED_11914483}}, adds the Publication Abstract to the page
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{{ABSTRACT_PUBMED_11914483}}


==About this Structure==
==About this Structure==
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[[Category: Sundaralingam, M.]]
[[Category: Sundaralingam, M.]]
[[Category: Drug binding]]
[[Category: Drug binding]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 14:20:05 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 23:41:15 2008''

Revision as of 20:41, 30 June 2008

File:1dvl.png

Template:STRUCTURE 1dvl

CRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COMPLEX WITH ONLY ONE DRUG BOUND AT ONE END

Template:ABSTRACT PUBMED 11914483

About this Structure

Full crystallographic information is available from OCA.

Reference

Structure of the 1:1 netropsin-decamer d(CCIICICCII)2 complex with a single bound netropsin., Shi K, Mitra SN, Sundaralingam M, Acta Crystallogr D Biol Crystallogr. 2002 Apr;58(Pt 4):601-6. Epub 2002, Mar 22. PMID:11914483

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