5cad: Difference between revisions

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 ==Crystal structure of the vicilin from Solanum melongena revealed existence of different anionic ligands in structurally similar pockets==
-<StructureSection load='5cad' size='340' side='right' caption='[[5cad]], [[Resolution|resolution]] 1.49&Aring;' scene=''>
+<StructureSection load='5cad' size='340' side='right'caption='[[5cad]], [[Resolution|resolution]] 1.49&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5cad]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Solanum_melongena Solanum melongena]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CAD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CAD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5cad]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_melongena Solanum melongena]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CAD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</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]] 1.49&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></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=5cad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cad OCA], [http://pdbe.org/5cad PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cad RCSB], [http://www.ebi.ac.uk/pdbsum/5cad PDBsum]</span></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=5cad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cad OCA], [https://pdbe.org/5cad PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cad RCSB], [https://www.ebi.ac.uk/pdbsum/5cad PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cad ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/A0A158RFR1_SOLME A0A158RFR1_SOLME]
-Crystal structure of a vicilin, SM80.1, was determined towards exploring its possible physiological functions. The protein was purified from Solanum melongena by combination of ammonium sulphate fractionation and size exclusion chromatography. Structure was determined ab initio at resolution of 1.5 A by X-ray crystallography showing the three-dimensional topology of the trimeric protein. Each monomer of SM80.1 consists of two similar domains with hydrophobic binding pocket and each accommodating different ligands, i.e. acetate and pyroglutamate. The relatively high stability of these independent anionic ligands in similar pockets indicated a strict requirement of stabilization by hydrogen bonds with the charged residues, suggesting a degree of plasticity within the binding pocket. Comparison of SM80.1 structure with those of other 7S vicilins indicated conservation of putative binding pocket for anionic ligands. Here we propose the possibility of trapping of these ligands in the protein for their requirement in the metabolic processes.
-Crystal structure of the vicilin from Solanum melongena reveals existence of different anionic ligands in structurally similar pockets.,Jain A, Kumar A, Salunke DM Sci Rep. 2016 Mar 23;6:23600. doi: 10.1038/srep23600. PMID:27004988<ref>PMID:27004988</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5cad" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Solanum melongena]]
-[[Category: Jain, A]]
+[[Category: Jain A]]
-[[Category: Kumar, A]]
+[[Category: Kumar A]]
-[[Category: Salunke, D M]]
+[[Category: Salunke DM]]
-[[Category: 7s vicilin]]
-[[Category: Plant protein]]
-[[Category: Sm80 1]]
-[[Category: Solanaceae]]