1nxd: Difference between revisions

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-[[Image:1nxd.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1nxd", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_1nxd|  PDB=1nxd  |  SCENE=  }}
-'''Crystal structure of MnMn Concanavalin A'''
+==Crystal structure of MnMn Concanavalin A==
+<StructureSection load='1nxd' size='340' side='right'caption='[[1nxd]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1nxd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Canavalia_ensiformis Canavalia ensiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NXD 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]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=1nxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nxd OCA], [https://pdbe.org/1nxd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nxd RCSB], [https://www.ebi.ac.uk/pdbsum/1nxd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nxd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CONA_CANEN CONA_CANEN] D-mannose 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/nx/1nxd_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1nxd ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Concanavalin A has been crystallized in the presence of the ligand (6-S-beta-D-galactopyranosyl-6-thio)-cyclomaltoheptaose. The crystals are isomorphous to those reported for ConA complexed with peptides at low resolution (3.00-2.75 angstroms). The structure was solved at 1.9 angstroms, with free R and R values of 0.201 and 0.184, respectively. As expected, no molecules of the ligand were bound to the protein. Soaking in the cryobuffer left its fingerprint as 25 molecules of glycerol in the bound solvent, most of them at specific positions. The fact that a glycerol molecule is located in the sugar-binding pocket of each of the four subunits in the asymmetric unit and another is located in two of the peptide-binding sites suggests a recognition phenomenon rather than a displacement of water molecules by glycerol. Crystal contact analysis shows that a relation exists between the residues that form hydrogen bonds to other asymmetric units and the space group: contact Asp58-Ser62 is a universal feature of ConA crystals, while Ser66-His121, Asn69-Asn118 and Tyr100-His205 contacts are general features of the C222(1) crystal form.
-==Overview==
+Structure of concanavalin A at pH 8: bound solvent and crystal contacts.,Lopez-Jaramillo FJ, Gonzalez-Ramirez LA, Albert A, Santoyo-Gonzalez F, Vargas-Berenguel A, Otalora F Acta Crystallogr D Biol Crystallogr. 2004 Jun;60(Pt 6):1048-56. Epub 2004, May 21. PMID:15159564<ref>PMID:15159564</ref>
-Concanavalin A has been crystallized in the presence of the ligand (6-S-beta-D-galactopyranosyl-6-thio)-cyclomaltoheptaose. The crystals are isomorphous to those reported for ConA complexed with peptides at low resolution (3.00-2.75 angstroms). The structure was solved at 1.9 angstroms, with free R and R values of 0.201 and 0.184, respectively. As expected, no molecules of the ligand were bound to the protein. Soaking in the cryobuffer left its fingerprint as 25 molecules of glycerol in the bound solvent, most of them at specific positions. The fact that a glycerol molecule is located in the sugar-binding pocket of each of the four subunits in the asymmetric unit and another is located in two of the peptide-binding sites suggests a recognition phenomenon rather than a displacement of water molecules by glycerol. Crystal contact analysis shows that a relation exists between the residues that form hydrogen bonds to other asymmetric units and the space group: contact Asp58-Ser62 is a universal feature of ConA crystals, while Ser66-His121, Asn69-Asn118 and Tyr100-His205 contacts are general features of the C222(1) crystal form.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-NXD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Canavalia_ensiformis Canavalia ensiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NXD OCA].
+</div>
+<div class="pdbe-citations 1nxd" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structure of concanavalin A at pH 8: bound solvent and crystal contacts., Lopez-Jaramillo FJ, Gonzalez-Ramirez LA, Albert A, Santoyo-Gonzalez F, Vargas-Berenguel A, Otalora F, Acta Crystallogr D Biol Crystallogr. 2004 Jun;60(Pt 6):1048-56. Epub 2004, May 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15159564 15159564]
+*[[Concanavalin 3D structures|Concanavalin 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Canavalia ensiformis]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Albert, A.]]
+[[Category: Albert A]]
-[[Category: Gonzalez-Ramirez, L A.]]
+[[Category: Gonzalez-Ramirez LA]]
-[[Category: Lopez-Jaramillo, F J.]]
+[[Category: Lopez-Jaramillo FJ]]
-[[Category: Otalora, F.]]
+[[Category: Otalora F]]
-[[Category: Santoyo-Gonzalez, F.]]
+[[Category: Santoyo-Gonzalez F]]
-[[Category: Vargas-Berenguel, A.]]
+[[Category: Vargas-Berenguel A]]
-[[Category: Lectin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 03:05:31 2008''