1ugw: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1ugw.png|left|200px]]
-<!--
+==Crystal structure of jacalin- Gal complex==
-The line below this paragraph, containing "STRUCTURE_1ugw", creates the "Structure Box" on the page.
+<StructureSection load='1ugw' size='340' side='right'caption='[[1ugw]], [[Resolution|resolution]] 1.70&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'>[[1ugw]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Artocarpus_integer Artocarpus integer]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UGW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UGW 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]] 1.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene></td></tr>
-{{STRUCTURE_1ugw|  PDB=1ugw  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ugw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ugw OCA], [https://pdbe.org/1ugw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ugw RCSB], [https://www.ebi.ac.uk/pdbsum/1ugw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ugw ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LECA_ARTIN LECA_ARTIN] D-galactose-specific lectin, binds the T-antigen structure Gal-beta1,3-GalNAc (Thomsen-Friedenreich-antigen-specific lectin). Potent and selective stimulant of distinct T- and B-cell functions. Shows a unique ability to specifically recognize IgA-1 from human serum.
+== 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/ug/1ugw_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=1ugw ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structures of the complexes of tetrameric jacalin with Gal, Me-alpha-GalNAc, Me-alpha-T-antigen, GalNAcbeta1-3Gal-alpha-O-Me and Galalpha1-6Glc (mellibiose) show that the sugar-binding site of jacalin has three components: the primary site, secondary site A, and secondary site B. In these structures and in the two structures reported earlier, Gal or GalNAc occupy the primary site with the anomeric carbon pointing towards secondary site A. The alpha-substituents, when present, interact, primarily hydrophobically, with secondary site A which has variable geometry. O-H..., centered pi and C-H...pi hydrogen bonds involving this site also exist. On the other hand, beta-substitution leads to severe steric clashes. Therefore, in complexes involving beta-linked disaccharides, the reducing sugar binds at the primary site with the non-reducing end located at secondary site B. The interactions at secondary site B are primarily through water bridges. Thus, the nature of the linkage determines the mode of the association of the sugar with jacalin. The interactions observed in the crystal structures and modeling based on them provide a satisfactory qualitative explanation of the available thermodynamic data on jacalin-carbohydrate interactions. They also lead to fresh insights into the nature of the binding of glycoproteins by jacalin.
-===Crystal structure of jacalin- Gal complex===
+Structural basis of the carbohydrate specificities of jacalin: an X-ray and modeling study.,Jeyaprakash AA, Katiyar S, Swaminathan CP, Sekar K, Surolia A, Vijayan M J Mol Biol. 2003 Sep 5;332(1):217-28. PMID:12946359<ref>PMID:12946359</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ugw" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12946359}}, adds the Publication Abstract to the page
+*[[Agglutinin 3D structures|Agglutinin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12946359 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12946359}}
+__TOC__
+</StructureSection>
-==About this Structure==
-UGW is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Artocarpus_integer Artocarpus integer]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UGW OCA].
-==Reference==
-Structural basis of the carbohydrate specificities of jacalin: an X-ray and modeling study., Jeyaprakash AA, Katiyar S, Swaminathan CP, Sekar K, Surolia A, Vijayan M, J Mol Biol. 2003 Sep 5;332(1):217-28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12946359 12946359]
 [[Category: Artocarpus integer]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Jeyaprakash, A A.]]
+[[Category: Jeyaprakash AA]]
-[[Category: Katiyar, S.]]
+[[Category: Katiyar S]]
-[[Category: Sekar, K.]]
+[[Category: Sekar K]]
-[[Category: Surolia, A.]]
+[[Category: Surolia A]]
-[[Category: Swaminathan, C P.]]
+[[Category: Swaminathan CP]]
-[[Category: Vijayan, M.]]
+[[Category: Vijayan M]]
-[[Category: All beta sheet protein]]
-[[Category: Beta prism i fold]]
-[[Category: Galactose specific]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 07:48:56 2008''