2ajs: Difference between revisions

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-{{Seed}}
-[[Image:2ajs.png|left|200px]]
-<!--
+==Crystal structure of cocaine catalytic antibody 7A1 Fab' in complex with heptaethylene glycol==
-The line below this paragraph, containing "STRUCTURE_2ajs", creates the "Structure Box" on the page.
+<StructureSection load='2ajs' size='340' side='right'caption='[[2ajs]], [[Resolution|resolution]] 1.70&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'>[[2ajs]] is a 2 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=2AJS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AJS 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]] 1.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=P33:3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL'>P33</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_2ajs|  PDB=2ajs  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ajs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ajs OCA], [https://pdbe.org/2ajs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ajs RCSB], [https://www.ebi.ac.uk/pdbsum/2ajs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ajs ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/IGKC_MOUSE IGKC_MOUSE]
+== 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/aj/2ajs_consurf.spt"</scriptWhenChecked>
+    <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/main_output.php?pdb_ID=2ajs ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Antibody 7A1 hydrolyzes cocaine to produce nonpsychoactive metabolites ecgonine methyl ester and benzoic acid. Crystal structures of 7A1 Fab' and six complexes with substrate cocaine, the transition state analog, products ecgonine methyl ester and benzoic acid together and individually, as well as heptaethylene glycol have been analyzed at 1.5-2.3 angstroms resolution. Here, we present snapshots of the complete cycle of the cocaine hydrolytic reaction at atomic resolution. Significant structural rearrangements occur along the reaction pathway, but they are generally limited to the binding site, including the ligands themselves. Several interacting side chains either change their rotamers or alter their mobility to accommodate the different reaction steps. CDR loop movements (up to 2.3 angstroms) and substantial side chain rearrangements (up to 9 angstroms) alter the shape and size (approximately 320-500 angstroms3) of the antibody active site from "open" to "closed" to "open" for the substrate, transition state, and product states, respectively.
-===Crystal structure of cocaine catalytic antibody 7A1 Fab' in complex with heptaethylene glycol===
+Complete reaction cycle of a cocaine catalytic antibody at atomic resolution.,Zhu X, Dickerson TJ, Rogers CJ, Kaufmann GF, Mee JM, McKenzie KM, Janda KD, Wilson IA Structure. 2006 Feb;14(2):205-16. PMID:16472740<ref>PMID:16472740</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ajs" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16472740}}, adds the Publication Abstract to the page
+*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16472740 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16472740}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AJS OCA].
+[[Category: Mus musculus]]
+[[Category: Wilson IA]]
-==Reference==
+[[Category: Zhu X]]
-Complete reaction cycle of a cocaine catalytic antibody at atomic resolution., Zhu X, Dickerson TJ, Rogers CJ, Kaufmann GF, Mee JM, McKenzie KM, Janda KD, Wilson IA, Structure. 2006 Feb;14(2):205-16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16472740 16472740]
-[[Category: Wilson, I A.]]
-[[Category: Zhu, X.]]
-[[Category: Catalytic antibody]]
-[[Category: Cocaine]]
-[[Category: Fab]]
-[[Category: Heptaethylene glycol]]
-[[Category: Hydrolytic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 11:56:28 2008''