1r6j: Difference between revisions

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 ==Ultrahigh resolution Crystal Structure of syntenin PDZ2==
-<StructureSection load='1r6j' size='340' side='right' caption='[[1r6j]], [[Resolution|resolution]] 0.73&Aring;' scene=''>
+<StructureSection load='1r6j' size='340' side='right'caption='[[1r6j]], [[Resolution|resolution]] 0.73&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1r6j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R6J FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1r6j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R6J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R6J FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.73&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SDCBP OR MDA9 OR SYCL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1r6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r6j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1r6j RCSB], [http://www.ebi.ac.uk/pdbsum/1r6j PDBsum]</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=1r6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r6j OCA], [https://pdbe.org/1r6j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r6j RCSB], [https://www.ebi.ac.uk/pdbsum/1r6j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r6j ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SDCB1_HUMAN SDCB1_HUMAN]] Seems to function as an adapter protein. In adherens junctions may function to couple syndecans to cytoskeletal proteins or signaling components. Seems to couple transcription factor SOX4 to the IL-5 receptor (IL5RA). May also play a role in vesicular trafficking. Seems to be required for the targeting of TGFA to the cell surface in the early secretory pathway.<ref>PMID:10230395</ref> <ref>PMID:11179419</ref> <ref>PMID:11498591</ref>
+[https://www.uniprot.org/uniprot/SDCB1_HUMAN SDCB1_HUMAN] Seems to function as an adapter protein. In adherens junctions may function to couple syndecans to cytoskeletal proteins or signaling components. Seems to couple transcription factor SOX4 to the IL-5 receptor (IL5RA). May also play a role in vesicular trafficking. Seems to be required for the targeting of TGFA to the cell surface in the early secretory pathway.<ref>PMID:10230395</ref> <ref>PMID:11179419</ref> <ref>PMID:11498591</ref>
 == 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/r6/1r6j_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r6/1r6j_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=1r6j ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The crystal structure of the second PDZ domain of the scaffolding protein syntenin was solved using data extending to 0.73 A resolution. The crystallographic model, including the hydrogen atoms and the anisotropic displacement parameters, was refined to a conventional R-factor of 7.5% and Rfree of 8.7%, making it the most precise crystallographic model of a protein molecule to date. The model reveals discrete disorder in several places in the molecule, and significant plasticity of the peptide bond, with some omega angles deviating by nearly 20 degrees from planarity. Most hydrogen atoms are easily identifiable in the electron density and weak hydrogen bonds of the C-H...O type are clearly visible between the beta-strands. The study sets a new standard for high-resolution protein crystallography.
-The PDZ2 domain of syntenin at ultra-high resolution: bridging the gap between macromolecular and small molecule crystallography.,Kang BS, Devedjiev Y, Derewenda U, Derewenda ZS J Mol Biol. 2004 Apr 30;338(3):483-93. PMID:15081807<ref>PMID:15081807</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+==See Also==
-</div>
+*[[3D structures of syntenin|3D structures of syntenin]]
 == References ==
 <references/>
@@ Line 32: / Line 28: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Derewenda, U]]
+[[Category: Large Structures]]
-[[Category: Derewenda, Z S]]
+[[Category: Derewenda U]]
-[[Category: Devedjiev, Y]]
+[[Category: Derewenda ZS]]
-[[Category: Kang, B S]]
+[[Category: Devedjiev Y]]
-[[Category: Membrane protein]]
+[[Category: Kang BS]]
-[[Category: Pdz]]