2dvb: Difference between revisions

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-[[Image:2dvb.png|left|200px]]
-{{STRUCTURE_2dvb|  PDB=2dvb  |  SCENE=  }}
+==Crystal structure of peanut lectin GAl-beta-1,6-GalNAc complex==
+<StructureSection load='2dvb' size='340' side='right'caption='[[2dvb]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2dvb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arachis_hypogaea Arachis hypogaea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DVB 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]] 2.25&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2dvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dvb OCA], [https://pdbe.org/2dvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dvb RCSB], [https://www.ebi.ac.uk/pdbsum/2dvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dvb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LECG_ARAHY LECG_ARAHY] D-galactose specific lectin.
+== 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/dv/2dvb_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2dvb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Crystal structures of peanut lectin complexed with Galbeta1-3Gal, methyl-T-antigen, Galbeta1-6GalNAc, Galalpha1-3Gal and Galalpha1-6Glc and that of a crystal grown in the presence of Galalpha1-3Galbeta1-4Gal have been determined using data collected at 100 K. The use of water bridges as a strategy for generating carbohydrate specificity was previously deduced from the complexes of the lectin with lactose (Galbeta1-4Glc) and T-antigen (Galbeta1-3GalNAc). This has been confirmed by the analysis of the complexes with Galbeta1-3Gal and methyl-T-antigen (Galbeta1-3GalNAc-alpha-OMe). A detailed analysis of lectin-sugar interactions in the complexes shows that they are more extensive when the beta-anomer is involved in the linkage. As expected, the second sugar residue is ill-defined when the linkage is 1--&gt;6. There are more than two dozen water molecules which occur in the hydration shells of all structures determined at resolutions better than 2.5 A. Most of them are involved in stabilizing the structure, particularly loops. Water molecules involved in lectin-sugar interactions are also substantially conserved. The lectin molecule is fairly rigid and does not appear to be affected by changes in temperature.
-===Crystal structure of peanut lectin GAl-beta-1,6-GalNAc complex===
+Structural studies on peanut lectin complexed with disaccharides involving different linkages: further insights into the structure and interactions of the lectin.,Natchiar SK, Srinivas O, Mitra N, Surolia A, Jayaraman N, Vijayan M Acta Crystallogr D Biol Crystallogr. 2006 Nov;62(Pt 11):1413-21. Epub 2006, Oct 18. PMID:17057347<ref>PMID:17057347</ref>
-{{ABSTRACT_PUBMED_17057347}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2dvb" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[2dvb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arachis_hypogaea Arachis hypogaea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DVB OCA].
+*[[Agglutinin 3D structures|Agglutinin 3D structures]]
+*[[Galactose-binding lectin|Galactose-binding lectin]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:017057347</ref><ref group="xtra">PMID:008278370</ref><ref group="xtra">PMID:008656429</ref><ref group="xtra">PMID:014747696</ref><references group="xtra"/>
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Arachis hypogaea]]
-[[Category: Jayaraman, N.]]
+[[Category: Large Structures]]
-[[Category: Mitra, N.]]
+[[Category: Jayaraman N]]
-[[Category: Natchiar, S K.]]
+[[Category: Mitra N]]
-[[Category: Srinivas, O.]]
+[[Category: Natchiar SK]]
-[[Category: Surolia, A.]]
+[[Category: Srinivas O]]
-[[Category: Vijayan, M.]]
+[[Category: Surolia A]]
-[[Category: Agglutinin]]
+[[Category: Vijayan M]]
-[[Category: Carbohydrate specificity]]
-[[Category: Legume lectin]]
-[[Category: Open quaternary structure]]
-[[Category: Sugar binding protein]]