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3kod

From Proteopedia

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{{Seed}}
 
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[[Image:3kod.png|left|200px]]
 
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<!--
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==DTD from Plasmodium falciparum in complex with D-Serine==
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The line below this paragraph, containing "STRUCTURE_3kod", creates the "Structure Box" on the page.
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<StructureSection load='3kod' size='340' side='right'caption='[[3kod]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3kod]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_falciparum_3D7 Plasmodium falciparum 3D7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KOD FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 3&#8491;</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=DSN:D-SERINE'>DSN</scene></td></tr>
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{{STRUCTURE_3kod| PDB=3kod | SCENE= }}
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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=3kod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kod OCA], [https://pdbe.org/3kod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kod RCSB], [https://www.ebi.ac.uk/pdbsum/3kod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kod ProSAT]</span></td></tr>
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</table>
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===DTD from Plasmodium falciparum in complex with D-Serine===
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== Function ==
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[https://www.uniprot.org/uniprot/DTD_PLAF7 DTD_PLAF7] D-aminoacyl-tRNA deacylase, with no observable activity on tRNAs charged with their cognate L-amino acid (PubMed:20007323, PubMed:24302572, PubMed:27224426). Probably acts by rejecting L-amino acids from its binding site rather than specific recognition of D-amino acids (PubMed:27224426). Catalyzes the hydrolysis of D-tyrosyl-tRNA(Tyr), has no activity on correctly charged L-tyrosyl-tRNA(Tyr) (PubMed:20007323, PubMed:24302572, PubMed:27224426). Hydrolyzes correctly charged, achiral, glycyl-tRNA(Gly) (PubMed:27224426). Deacylates mischarged D.melanogaster and E.coli glycyl-tRNA(Ala) (PubMed:28362257). Probably acts via tRNA-based rather than protein-based catalysis (PubMed:24302572, PubMed:27224426). Acts on tRNAs only when the D-amino acid is either attached to the ribose 3'-OH or transferred to the 3'-OH from the 2'-OH through rapid transesterification (PubMed:24302572). Binds a number of other D-amino acids (D-Arg, D-Glu, D-His, D-Lys, D-Ser), suggesting it may also deacylate other mischarged tRNAs (PubMed:20007323).<ref>PMID:20007323</ref> <ref>PMID:24302572</ref> <ref>PMID:27224426</ref> <ref>PMID:28362257</ref>
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== Evolutionary Conservation ==
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==About this Structure==
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[[Image:Consurf_key_small.gif|200px|right]]
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3KOD is a 6 chains structure with sequences from [http://en.wikipedia.org/wiki/Plasmodium_falciparum_3d7 Plasmodium falciparum 3d7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KOD OCA].
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Check<jmol>
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[[Category: Plasmodium falciparum 3d7]]
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<jmolCheckbox>
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[[Category: Bhatt, T K.]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ko/3kod_consurf.spt"</scriptWhenChecked>
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[[Category: Manickam, Y.]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: Sharma, A.]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: D-amino acid]]
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</jmolCheckbox>
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[[Category: D-serine]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3kod ConSurf].
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[[Category: Deacylase]]
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<div style="clear:both"></div>
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[[Category: Dtd]]
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== References ==
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[[Category: Hydrolase]]
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<references/>
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__TOC__
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 28 14:35:12 2010''
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Plasmodium falciparum 3D7]]
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[[Category: Bhatt TK]]
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[[Category: Manickam Y]]
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[[Category: Sharma A]]

Current revision

DTD from Plasmodium falciparum in complex with D-Serine

PDB ID 3kod

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