1my0: Difference between revisions

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-{{Seed}}
-[[Image:1my0.png|left|200px]]
-<!--
+==crystal titration experiments (AMPA co-crystals soaked in 100 nM BrW)==
-The line below this paragraph, containing "STRUCTURE_1my0", creates the "Structure Box" on the page.
+<StructureSection load='1my0' size='340' side='right'caption='[[1my0]], [[Resolution|resolution]] 1.90&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'>[[1my0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MY0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MY0 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]] 1.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1my0|  PDB=1my0  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1my0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1my0 OCA], [https://pdbe.org/1my0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1my0 RCSB], [https://www.ebi.ac.uk/pdbsum/1my0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1my0 ProSAT]</span></td></tr>
+</table>
+== 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/my/1my0_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=1my0 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Numerous naturally occurring and synthetic alpha-amino acids act as agonists on (S)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazole) propionic acid (AMPA) receptors but nevertheless display significant differences in their functional properties and modes of interaction. The 5-substituted willardiines are a series of compounds that exhibit a range of affinities, act as partial agonists, and give rise to intermediate levels of activation and desensitization. However, the molecular basis for the activities of 5-substituted willardiines has not been conclusively elaborated at the level of atomic resolution. Here we provide insight into the molecular basis of the potency and efficacy elicited by the 5-substituted willardiines on the basis of cocrystal structures with the GluR2 ligand-binding core. We also show that the crystallized ligand-binding core has an affinity for agonists similar to the ligand-binding core in solution. Analysis of multiple crystal lattices suggests modes by which the ligand-binding core dimers interact in the tetrameric receptor. These studies further our understanding of how subtle differences in the structures of agonists are correlated to changes in the conformation of residues and water molecules in the immediate binding pocket and to the degree of domain closure.
-===crystal titration experiments (AMPA co-crystals soaked in 100 nM BrW)===
+Probing the function, conformational plasticity, and dimer-dimer contacts of the GluR2 ligand-binding core: studies of 5-substituted willardiines and GluR2 S1S2 in the crystal.,Jin R, Gouaux E Biochemistry. 2003 May 13;42(18):5201-13. PMID:12731861<ref>PMID:12731861</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1my0" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12731861}}, adds the Publication Abstract to the page
+*[[Glutamate receptor 3D structures|Glutamate receptor 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12731861 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12731861}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-MY0 is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MY0 OCA].
-==Reference==
-<ref group="xtra">PMID:12731861</ref><references group="xtra"/>
 [[Category: Rattus norvegicus]]
-[[Category: Gouaux, E.]]
+[[Category: Gouaux E]]
-[[Category: Jin, R.]]
+[[Category: Jin R]]
-[[Category: Ampa]]
-[[Category: Bromo-willardiine]]
-[[Category: Crystal titration]]
-[[Category: Glur2]]
-[[Category: Ionotropic glutamate receptor]]
-[[Category: Ligand binding core]]
-[[Category: Partial agonist]]
-[[Category: S1s2]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 19:51:55 2009''