1dvl

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==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==
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<StructureSection load='1dvl' size='340' side='right' caption='[[1dvl]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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<StructureSection load='1dvl' size='340' side='right'caption='[[1dvl]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DVL FirstGlance]. <br>
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<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>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NT:NETROPSIN'>NT</scene><br>
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</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>
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<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr>
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<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>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dvl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dvl RCSB], [http://www.ebi.ac.uk/pdbsum/1dvl PDBsum]</span></td></tr>
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<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>
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<table>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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<ref>PMID:11914483</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Mitra, S N.]]
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[[Category: Large Structures]]
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[[Category: Shi, K.]]
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[[Category: Mitra SN]]
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[[Category: Sundaralingam, M.]]
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[[Category: Shi K]]
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[[Category: Dna]]
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[[Category: Sundaralingam M]]
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[[Category: Drug binding]]
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Current revision

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

PDB ID 1dvl

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