2r3d: Difference between revisions

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-{{Seed}}
-[[Image:2r3d.png|left|200px]]
-<!--
+==Ricin A-chain (recombinant) complex with Acetamide==
-The line below this paragraph, containing "STRUCTURE_2r3d", creates the "Structure Box" on the page.
+<StructureSection load='2r3d' size='340' side='right'caption='[[2r3d]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2r3d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1zb2 1zb2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R3D FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.09&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACM:ACETAMIDE'>ACM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_2r3d|  PDB=2r3d  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2r3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r3d OCA], [https://pdbe.org/2r3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r3d RCSB], [https://www.ebi.ac.uk/pdbsum/2r3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r3d ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RICI_RICCO RICI_RICCO] Ricin is highly toxic to animal cells and to a lesser extent to plant cells. The A chain acts as a glycosidase that removes a specific adenine residue from an exposed loop of the 28S rRNA (A4324 in mammals), leading to rRNA breakage. As this loop is involved in elongation factor binding, modified ribosomes are catalytically inactive and unable to support protein synthesis. The A chain can inactivate a few thousand ribosomes per minute, faster than the cell can make new ones. Therefore a single A chain molecule can kill an animal cell. The B chain binds to beta-D-galactopyranoside moieties on cell surface glycoproteins and glycolipids and facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (Lectin activity).
+== 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/r3/2r3d_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/main_output.php?pdb_ID=2r3d ConSurf].
+<div style="clear:both"></div>
-===Ricin A-chain (recombinant) complex with Acetamide===
+==See Also==
+*[[Ricin 3D structures|Ricin 3D structures]]
+__TOC__
-<!--
+</StructureSection>
-The line below this paragraph, {{ABSTRACT_PUBMED_17986339}}, adds the Publication Abstract to the page
+[[Category: Large Structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17986339 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_17986339}}
-==About this Structure==
-R3D is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1zb2 1zb2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R3D OCA].
-==Reference==
-<ref group="xtra">PMID:17986339</ref><references group="xtra"/>
 [[Category: Ricinus communis]]
-[[Category: RRNA N-glycosylase]]
+[[Category: Carra JH]]
-[[Category: Carra, J H.]]
+[[Category: Machiesky LM]]
-[[Category: Machiesky, L M.]]
+[[Category: McHugh CA]]
-[[Category: McHugh, C A.]]
+[[Category: Millard CB]]
-[[Category: Millard, C B.]]
+[[Category: Mulligan S]]
-[[Category: Mulligan, S.]]
+[[Category: Soares AS]]
-[[Category: Soares, A S.]]
-[[Category: Glycoprotein]]
-[[Category: Hydrolase]]
-[[Category: Lectin]]
-[[Category: N-glycosidase]]
-[[Category: Plant defense]]
-[[Category: Protein synthesis inhibitor]]
-[[Category: Ricin]]
-[[Category: Ricinus communi]]
-[[Category: Toxin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 08:23:59 2009''