3dmm: Difference between revisions

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 ==Crystal structure of the CD8 alpha beta/H-2Dd complex==
-<StructureSection load='3dmm' size='340' side='right' caption='[[3dmm]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='3dmm' size='340' side='right'caption='[[3dmm]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3dmm]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DMM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DMM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3dmm]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DMM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DMM FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">H2-D1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus]), B2m ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus]), Cd8a, Lyt-2, Lyt2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus]), Cd8b, Cd8b1, Ly-3, Lyt-3, Lyt3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])</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]] 2.6&#8491;</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=3dmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dmm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dmm RCSB], [http://www.ebi.ac.uk/pdbsum/3dmm 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=3dmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dmm OCA], [https://pdbe.org/3dmm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dmm RCSB], [https://www.ebi.ac.uk/pdbsum/3dmm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dmm ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CD8A_MOUSE CD8A_MOUSE]] Identifies cytotoxic/suppressor T-cells that interact with MHC class I bearing targets. CD8 is thought to play a role in the process of T-cell mediated killing. CD8 alpha chains binds to class I MHC molecules alpha-3 domains. [[http://www.uniprot.org/uniprot/HA12_MOUSE HA12_MOUSE]] Involved in the presentation of foreign antigens to the immune system. [[http://www.uniprot.org/uniprot/Q91XJ8_MOUSE Q91XJ8_MOUSE]] Component of the class I major histocompatibility complex (MHC). Involved in the presentation of peptide antigens to the immune system. [[http://www.uniprot.org/uniprot/CD8B_MOUSE CD8B_MOUSE]] Identifies cytotoxic/suppressor T-cells that interact with MHC class I bearing targets. CD8 is thought to play a role in the process of T-cell mediated killing.
+[https://www.uniprot.org/uniprot/HA12_MOUSE HA12_MOUSE] Involved in the presentation of foreign antigens to the immune system.
 == 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/dm/3dmm_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dm/3dmm_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3dmm ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3dmm" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Beta-2 microglobulin|Beta-2 microglobulin]]
+*[[Beta-2 microglobulin 3D structures|Beta-2 microglobulin 3D structures]]
-*[[CD8|CD8]]
+*[[CD8 3D structures|CD8 3D structures]]
-*[[Major histocompatibility complex|Major histocompatibility complex]]
+*[[MHC 3D structures|MHC 3D structures]]
+*[[MHC I 3D structures|MHC I 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Margulies, D H]]
+[[Category: Margulies DH]]
-[[Category: Natarajan, K]]
+[[Category: Natarajan K]]
-[[Category: Wang, R]]
+[[Category: Wang R]]
-[[Category: Envelope protein]]
-[[Category: Glycoprotein]]
-[[Category: Immune response]]
-[[Category: Immune system]]
-[[Category: Immunoglobulin domain]]
-[[Category: Membrane]]
-[[Category: Mhc i]]
-[[Category: Phosphoprotein]]
-[[Category: Secreted]]
-[[Category: T cell co-receptor cd8ab mhc complex]]
-[[Category: Transmembrane]]