1v6k: Difference between revisions

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-{{Seed}}
-[[Image:1v6k.png|left|200px]]
-<!--
+==Peanut lectin-lactose complex in the presence of peptide(IWSSAGNVA)==
-The line below this paragraph, containing "STRUCTURE_1v6k", creates the "Structure Box" on the page.
+<StructureSection load='1v6k' size='340' side='right'caption='[[1v6k]], [[Resolution|resolution]] 2.40&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'>[[1v6k]] 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=1V6K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V6K 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]] 2.4&#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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PRD_900008:alpha-lactose'>PRD_900008</scene></td></tr>
-{{STRUCTURE_1v6k|  PDB=1v6k  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1v6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v6k OCA], [https://pdbe.org/1v6k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v6k RCSB], [https://www.ebi.ac.uk/pdbsum/1v6k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v6k 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/v6/1v6k_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=1v6k ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Until recently, it has only been possible to grow crystals of peanut lectin when complexed with sugar ligands. It is now shown that it is possible to grow peanut lectin crystals at acidic pH in the presence of oligopeptides corresponding to a loop in the lectin molecule. Crystals have also been prepared in the presence of these peptides as well as lactose. Low-pH crystal forms of the lectin-lactose complex similar to those obtained at neutral pH have also been grown. Thus, crystals of peanut lectin grown under different environmental conditions, at two pH values with and without sugar bound to the lectin, are now available. They have been used to explore the plasticity and hydration of the molecule. A detailed comparison between different structures shows that the lectin molecule is sturdy and that the effect of changes in pH, ligand binding and environment on it is small. The region involving the curved front beta-sheet and the loops around the second hydrophobic core is comparatively rigid. The back beta-sheet involved in quaternary association, which exhibits considerable variability, is substantially flexible, as is the sugar-binding region. The numbers of invariant water molecules in the hydration shell are small and they are mainly involved in metal coordination or in stabilizing unusual structural features. Small consistent movements occur in the combining site upon sugar binding, although the site is essentially preformed.
-===Peanut lectin-lactose complex in the presence of peptide(IWSSAGNVA)===
+Structural plasticity of peanut lectin: an X-ray analysis involving variation in pH, ligand binding and crystal structure.,Kundhavai Natchiar S, Arockia Jeyaprakash A, Ramya TN, Thomas CJ, Suguna K, Surolia A, Vijayan M Acta Crystallogr D Biol Crystallogr. 2004 Feb;60(Pt 2):211-9. Epub 2004, Jan 23. PMID:14747696<ref>PMID:14747696</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1v6k" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_14747696}}, adds the Publication Abstract to the page
+*[[Galactose-binding lectin|Galactose-binding lectin]]
-(as it appears on PubMed at http://www.pubmed.gov), where 14747696 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14747696}}
+__TOC__
+</StructureSection>
-==About this Structure==
-V6K is a [[Single protein]] structure of 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=1V6K OCA].
-==Reference==
-Structural plasticity of peanut lectin: an X-ray analysis involving variation in pH, ligand binding and crystal structure., Kundhavai Natchiar S, Arockia Jeyaprakash A, Ramya TN, Thomas CJ, Suguna K, Surolia A, Vijayan M, Acta Crystallogr D Biol Crystallogr. 2004 Feb;60(Pt 2):211-9. Epub 2004, Jan 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14747696 14747696]
-Conformation, protein-carbohydrate interactions and a novel subunit association in the refined structure of peanut lectin-lactose complex., Banerjee R, Das K, Ravishankar R, Suguna K, Surolia A, Vijayan M, J Mol Biol. 1996 Jun 7;259(2):281-96. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8656429 8656429]
-Crystal structures of the peanut lectin-lactose complex at acidic pH: retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal packing directed by interactions at the combining site., Ravishankar R, Thomas CJ, Suguna K, Surolia A, Vijayan M, Proteins. 2001 May 15;43(3):260-70. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11288176 11288176]
 [[Category: Arachis hypogaea]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Jeyaprakash, A Arockia.]]
+[[Category: Arockia Jeyaprakash A]]
-[[Category: Natchiar, S Kundhavai.]]
+[[Category: Kundhavai Natchiar S]]
-[[Category: Ramya, T N.C.]]
+[[Category: Ramya TNC]]
-[[Category: Suguna, K.]]
+[[Category: Suguna K]]
-[[Category: Surolia, A.]]
+[[Category: Surolia A]]
-[[Category: Thomas, C J.]]
+[[Category: Thomas CJ]]
-[[Category: Vijayan, M.]]
+[[Category: Vijayan M]]
-[[Category: Agglutinin]]
-[[Category: Carbohydrate specificity]]
-[[Category: Lectin]]
-[[Category: Open quaternary association]]
-[[Category: Orthorhombic]]
-[[Category: Peptide]]
-[[Category: Protein crystallography]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 13:29:13 2008''