1ivs: Difference between revisions

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 ==CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE==
-<StructureSection load='1ivs' size='340' side='right' caption='[[1ivs]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='1ivs' size='340' side='right'caption='[[1ivs]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ivs]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IVS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ivs]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IVS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IVS FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=VAA:N-[VALINYL]-N-[ADENOSYL]-DIAMINOSUFONE'>VAA</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">valS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VAA:N-[VALINYL]-N-[ADENOSYL]-DIAMINOSUFONE'>VAA</scene></td></tr>
-<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ivs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ivs OCA], [https://pdbe.org/1ivs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ivs RCSB], [https://www.ebi.ac.uk/pdbsum/1ivs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ivs ProSAT], [https://www.topsan.org/Proteins/RSGI/1ivs TOPSAN]</span></td></tr>
-<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=1ivs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ivs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ivs RCSB], [http://www.ebi.ac.uk/pdbsum/1ivs PDBsum], [http://www.topsan.org/Proteins/RSGI/1ivs TOPSAN]</span></td></tr>
+</table>
-<table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYV_THETH SYV_THETH] Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a "posttransfer" editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner.[HAMAP-Rule:MF_02004]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iv/1ivs_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iv/1ivs_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1ivs ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1ivs" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Aminoacyl tRNA Synthetase|Aminoacyl tRNA Synthetase]]
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermus thermophilus]]
-[[Category: Valine--tRNA ligase]]
+[[Category: Fukai S]]
-[[Category: Fukai, S.]]
+[[Category: Nureki O]]
-[[Category: Nureki, O.]]
+[[Category: Sekine S-I]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Shimada A]]
-[[Category: Sekine, S I.]]
+[[Category: Vassylyev DG]]
-[[Category: Shimada, A.]]
+[[Category: Yokoyama S]]
-[[Category: Vassylyev, D G.]]
-[[Category: Yokoyama, S.]]
-[[Category: Beta barrel]]
-[[Category: Helix bundle]]
-[[Category: Ligase-rna complex]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rossmann fold]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]