1jot: Difference between revisions

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 ==STRUCTURE OF THE LECTIN MPA COMPLEXED WITH T-ANTIGEN DISACCHARIDE==
-<StructureSection load='1jot' size='340' side='right' caption='[[1jot]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='1jot' size='340' side='right'caption='[[1jot]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1jot]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Maclura_pomifera Maclura pomifera]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JOT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JOT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1jot]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Maclura_pomifera Maclura pomifera]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JOT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JOT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jot OCA], [http://pdbe.org/1jot PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jot RCSB], [http://www.ebi.ac.uk/pdbsum/1jot PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jot ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=PRD_900084:Thomsen-Friedenreich+antigen'>PRD_900084</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=1jot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jot OCA], [https://pdbe.org/1jot PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jot RCSB], [https://www.ebi.ac.uk/pdbsum/1jot PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jot ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/LECA_MACPO LECA_MACPO]] D-galactose-specific lectin, binds the T-antigen structure Gal-beta1,3-GalNAc. [[http://www.uniprot.org/uniprot/LECB2_MACPO LECB2_MACPO]] D-galactose-specific lectin, binds the T-antigen structure Gal-beta1,3-GalNAc.
+[https://www.uniprot.org/uniprot/LECA_MACPO LECA_MACPO] D-galactose-specific lectin, binds the T-antigen structure Gal-beta1,3-GalNAc.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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 </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=1jot ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Maclura pomifera agglutinin is a tetrameric plant seed lectin with high affinity for the tumor-associated T-antigen disaccharide, Galbeta1,3GalNAcalpha, and hence for many O-linked glycopeptide structures. Unlike members of most lectin families, it lacks both metal ions and Cys residues. The structure of its complex with Galbeta1,3GalNAc was determined to 2.2 by first using multiwavelength anomalous diffraction with a lead derivative of the native protein, and then using molecular replacement with the unrefined structure as a model to solve the structure of the complex. The subunits share the beta-prism architecture and three-fold pseudo-symmetry of the related lectin jacalin, with the 21-residue beta-chains in the center of the tetramer. Interactions with the GalNAc predominate in the binding of the disaccharide. It forms a network of H-bonds with only one side chain, from an Asp residue, the amino group of the N-terminal Gly of the alpha-chain, and peptide backbone atoms of two aromatic residues. The Gal moiety does not H-bond directly with residues in the same monomer, i.e. there is no true subsite for it, but there are interactions through two water molecules. In the crystal, it interacts with residues in the binding site of an adjacent tetramer. The minimum energy conformation expected for the disaccharide is retained, despite its mediating the tetramer-tetramer interactions in the crystal packing. The resulting lattice is comparable to those seen for complexes of other lectins with branched glycopeptides.
-Structure of the complex of Maclura pomifera agglutinin and the T-antigen disaccharide, Galbeta1,3GalNAc.,Lee X, Thompson A, Zhang Z, Ton-that H, Biesterfeldt J, Ogata C, Xu L, Johnston RA, Young NM J Biol Chem. 1998 Mar 13;273(11):6312-8. PMID:9497359<ref>PMID:9497359</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1jot" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Agglutinin|Agglutinin]]
+*[[Agglutinin 3D structures|Agglutinin 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Maclura pomifera]]
-[[Category: Biesterfeldt, J]]
+[[Category: Biesterfeldt J]]
-[[Category: Hoa, T T]]
+[[Category: Hoa T-T]]
-[[Category: Johnston, R A.Z]]
+[[Category: Johnston RAZ]]
-[[Category: Lee, X]]
+[[Category: Lee X]]
-[[Category: Ogata, C]]
+[[Category: Ogata C]]
-[[Category: Thompson, A]]
+[[Category: Thompson A]]
-[[Category: Xu, L]]
+[[Category: Xu L]]
-[[Category: Young, N M]]
+[[Category: Young NM]]
-[[Category: Zhang, Z]]
+[[Category: Zhang Z]]
-[[Category: Beta prism]]
-[[Category: Lectin]]
-[[Category: T-antigen]]