1ncw: Difference between revisions

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-[[Image:1ncw.jpg|left|200px]]
- {{Structure
+==Cationic Cyclization Antibody 4C6 in Complex with Benzoic Acid==
-|PDB= 1ncw |SIZE=350|CAPTION= <scene name='initialview01'>1ncw</scene>, resolution 1.30&Aring;
+<StructureSection load='1ncw' size='340' side='right'caption='[[1ncw]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
+<table><tr><td colspan='2'>[[1ncw]] 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=1NCW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NCW FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#8491;</td></tr>
-|GENE=
+<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=GOL:GLYCEROL'>GOL</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=1ncw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ncw OCA], [https://pdbe.org/1ncw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ncw RCSB], [https://www.ebi.ac.uk/pdbsum/1ncw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ncw ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q58EU8_MOUSE Q58EU8_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/nc/1ncw_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=1ncw ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Antibody 4C6 efficiently catalyzes a cationic cyclization reaction. Crystal structures of the antibody 4C6 Fab in complex with benzoic acid and in complex with its eliciting hapten were determined to 1.30A and 2.45A resolution, respectively. These crystal structures, together with computational analysis, have elucidated a possible mechanism for the monocyclization reaction. The hapten complex revealed a combining site pocket with high shape complementarity to the hapten. This active site cleft is dominated by aromatic residues that shield the highly reactive carbocation intermediates from solvent and stabilize the carbocation intermediates through cation-pi interactions. Modeling of an acyclic olefinic sulfonate ester substrate and the transition state (TS) structures shows that the chair-like transition state is favored, and trapping by water directly produces trans-2-(dimethylphenylsilyl)-cyclohexanol, whereas the less favored boat-like transition state leads to cyclohexene. The only significant change observed upon hapten binding is a side-chain rotation of Trp(L89), which reorients to form the base of the combining site. Intriguingly, a benzoic acid molecule was sequestered in the combining site of the unliganded antibody. The 4C6 active site was compared to that observed in a previously reported tandem cyclization antibody 19A4 hapten complex. These cationic cyclization antibodies exhibit convergent structural features with terpenoid cyclases that appear to be important for catalysis.
-'''CATIONIC CYCLIZATION ANTIBODY 4C6 IN COMPLEX WITH BENZOIC ACID'''
+Structural basis for antibody catalysis of a cationic cyclization reaction.,Zhu X, Heine A, Monnat F, Houk KN, Janda KD, Wilson IA J Mol Biol. 2003 May 23;329(1):69-83. PMID:12742019<ref>PMID:12742019</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ncw" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Antibody 4C6 efficiently catalyzes a cationic cyclization reaction. Crystal structures of the antibody 4C6 Fab in complex with benzoic acid and in complex with its eliciting hapten were determined to 1.30A and 2.45A resolution, respectively. These crystal structures, together with computational analysis, have elucidated a possible mechanism for the monocyclization reaction. The hapten complex revealed a combining site pocket with high shape complementarity to the hapten. This active site cleft is dominated by aromatic residues that shield the highly reactive carbocation intermediates from solvent and stabilize the carbocation intermediates through cation-pi interactions. Modeling of an acyclic olefinic sulfonate ester substrate and the transition state (TS) structures shows that the chair-like transition state is favored, and trapping by water directly produces trans-2-(dimethylphenylsilyl)-cyclohexanol, whereas the less favored boat-like transition state leads to cyclohexene. The only significant change observed upon hapten binding is a side-chain rotation of Trp(L89), which reorients to form the base of the combining site. Intriguingly, a benzoic acid molecule was sequestered in the combining site of the unliganded antibody. The 4C6 active site was compared to that observed in a previously reported tandem cyclization antibody 19A4 hapten complex. These cationic cyclization antibodies exhibit convergent structural features with terpenoid cyclases that appear to be important for catalysis.
+*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-NCW is a [[Single protein]] structure of 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=1NCW OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-Structural basis for antibody catalysis of a cationic cyclization reaction., Zhu X, Heine A, Monnat F, Houk KN, Janda KD, Wilson IA, J Mol Biol. 2003 May 23;329(1):69-83. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12742019 12742019]
 [[Category: Mus musculus]]
-[[Category: Single protein]]
+[[Category: Wilson IA]]
-[[Category: Wilson, I A.]]
+[[Category: Zhu X]]
-[[Category: Zhu, X.]]
-[[Category: BEZ]]
-[[Category: GOL]]
-[[Category: catalytic antibody]]
-[[Category: cationic cyclization reaction]]
-[[Category: immunoglobulin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:55:13 2008''