2ak1: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2ak1.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2ak1", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_2ak1|  PDB=2ak1  |  SCENE=  }}
-'''Crystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Complex with benzoic acid'''
+==Crystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Complex with benzoic acid==
+<StructureSection load='2ak1' size='340' side='right'caption='[[2ak1]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2ak1]] 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=2AK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AK1 FirstGlance]. <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]] 1.85&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=2ak1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ak1 OCA], [https://pdbe.org/2ak1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ak1 RCSB], [https://www.ebi.ac.uk/pdbsum/2ak1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ak1 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/ak/2ak1_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=2ak1 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.
-==Overview==
+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>
-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.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AK1 OCA].
+</div>
+<div class="pdbe-citations 2ak1" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-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]
+*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
-[[Category: Wilson, I A.]]
+== References ==
-[[Category: Zhu, X.]]
+<references/>
-[[Category: Benzoic acid]]
+__TOC__
-[[Category: Catalytic antibody]]
+</StructureSection>
-[[Category: Fab]]
+[[Category: Large Structures]]
-[[Category: Hydrolytic]]
+[[Category: Mus musculus]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 19:08:52 2008''
+[[Category: Wilson IA]]
+[[Category: Zhu X]]