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New page: left|200px<br /><applet load="1dvl" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dvl, resolution 2.4Å" /> '''CRYSTAL STRUCTURE OF ...
 
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[[Image:1dvl.gif|left|200px]]<br /><applet load="1dvl" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1dvl, resolution 2.4&Aring;" />
'''CRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COMPLEX WITH ONLY ONE DRUG BOUND AT ONE END'''<br />


==Overview==
==CRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COMPLEX WITH ONLY ONE DRUG BOUND AT ONE END==
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.
<StructureSection load='1dvl' size='340' side='right'caption='[[1dvl]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1dvl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DVL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DVL FirstGlance]. <br>
1DVL is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with NT as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DVL OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NT:NETROPSIN'>NT</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dvl OCA], [https://pdbe.org/1dvl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dvl RCSB], [https://www.ebi.ac.uk/pdbsum/1dvl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dvl ProSAT]</span></td></tr>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11914483 11914483]
</table>
[[Category: Protein complex]]
__TOC__
[[Category: Mitra, S.N.]]
</StructureSection>
[[Category: Shi, K.]]
[[Category: Large Structures]]
[[Category: Sundaralingam, M.]]
[[Category: Mitra SN]]
[[Category: NT]]
[[Category: Shi K]]
[[Category: drug binding]]
[[Category: Sundaralingam M]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:44:17 2007''

Latest revision as of 06:59, 7 February 2024

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

1dvl, resolution 2.40Å

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