1mj7: Difference between revisions

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-[[Image:1mj7.png|left|200px]]
-<!--
+==Crystal Structure Of The Complex Of The Fab fragment of Esterolytic Antibody MS5-393 and A Transition-State Analog==
-The line below this paragraph, containing "STRUCTURE_1mj7", creates the "Structure Box" on the page.
+<StructureSection load='1mj7' size='340' side='right'caption='[[1mj7]], [[Resolution|resolution]] 2.25&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'>[[1mj7]] 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=1MJ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MJ7 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]] 2.25&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HAL:N-{[2-({[1-(4-CARBOXYBUTANOYL)AMINO]-2-PHENYLETHYL}-HYDROXYPHOSPHINYL)OXY]ACETYL}-2-PHENYLETHYLAMINE'>HAL</scene></td></tr>
-{{STRUCTURE_1mj7|  PDB=1mj7  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1mj7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mj7 OCA], [https://pdbe.org/1mj7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mj7 RCSB], [https://www.ebi.ac.uk/pdbsum/1mj7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mj7 ProSAT]</span></td></tr>
+</table>
+== 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/mj/1mj7_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=1mj7 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structures of four related Fab fragments of a family of catalytic antibodies displaying differential levels of esterase activity have been solved in the presence and in the absence of the transition-state analogue (TSA) that was used to elicit the immune response. The electron density maps show that the TSA conformation is essentially identical, with limited changes on hapten binding. Interactions with the TSA explain the specificity for the D rather than the L-isomer of the substrate. Differences in the residues in the hapten-binding pocket, which increase hydrophobicity, appear to correlate with an increase in the affinity of the antibodies for their substrate. Analysis of the structures at the active site reveals a network of conserved hydrogen bond contacts between the TSA and the antibodies, and points to a critical role of two conserved residues, HisL91 and LysH95, in catalysis. However, these two key residues are set into very different contexts in their respective structures, with an apparent direct correlation between the catalytic power of the antibodies and the complexity of their interactions with the rest of the protein. This suggests that the catalytic efficiency may be controlled by contacts arising from a second sphere of residues at the periphery of the active site.
-===Crystal Structure Of The Complex Of The Fab fragment of Esterolytic Antibody MS5-393 and A Transition-State Analog===
+High-resolution crystal structure of the Fab-fragments of a family of mouse catalytic antibodies with esterase activity.,Ruzheinikov SN, Muranova TA, Sedelnikova SE, Partridge LJ, Blackburn GM, Murray IA, Kakinuma H, Takahashi-Ando N, Shimazaki K, Sun J, Nishi Y, Rice DW J Mol Biol. 2003 Sep 12;332(2):423-35. PMID:12948492<ref>PMID:12948492</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1mj7" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12948492}}, adds the Publication Abstract to the page
+*[[Adaptin 3D structures|Adaptin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12948492 is the PubMed ID number.
+*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_12948492}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-[[1mj7]] is a 2 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=1MJ7 OCA].
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:012948492</ref><references group="xtra"/>
 [[Category: Mus musculus]]
-[[Category: Blackburn, G M.]]
+[[Category: Blackburn GM]]
-[[Category: Kakinuma, H.]]
+[[Category: Kakinuma H]]
-[[Category: Muranova, T A.]]
+[[Category: Muranova TA]]
-[[Category: Murray, I A.]]
+[[Category: Murray IA]]
-[[Category: Nishi, Y.]]
+[[Category: Nishi Y]]
-[[Category: Partridge, L J.]]
+[[Category: Partridge LJ]]
-[[Category: Rice, D W.]]
+[[Category: Rice DW]]
-[[Category: Ruzheinikov, S N.]]
+[[Category: Ruzheinikov SN]]
-[[Category: Sedelnikova, S E.]]
+[[Category: Sedelnikova SE]]
-[[Category: Shimazaki, K.]]
+[[Category: Shimazaki K]]
-[[Category: Sun, J.]]
+[[Category: Sun J]]
-[[Category: Takashi, N.]]
+[[Category: Takashi N]]
-[[Category: Catalytic antibody]]
-[[Category: Ester hydrolysis]]
-[[Category: Esterolytic]]
-[[Category: Fab]]
-[[Category: Immune system]]
-[[Category: Immunoglobulin]]
-[[Category: Tsa]]