4xv6: Difference between revisions

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 ==CcP gateless cavity==
-<StructureSection load='4xv6' size='340' side='right' caption='[[4xv6]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
+<StructureSection load='4xv6' size='340' side='right'caption='[[4xv6]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4xv6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XV6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XV6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4xv6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XV6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XV6 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.55&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xv4|4xv4]], [[4xv5|4xv5]], [[4xv7|4xv7]], [[4xv8|4xv8]], [[4xva|4xva]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CCP1, CCP, CPO, YKR066C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=4xv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xv6 OCA], [https://pdbe.org/4xv6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xv6 RCSB], [https://www.ebi.ac.uk/pdbsum/4xv6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xv6 ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4xv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xv6 OCA], [http://pdbe.org/4xv6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xv6 RCSB], [http://www.ebi.ac.uk/pdbsum/4xv6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xv6 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
+[https://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Interrogating fragment libraries by X-ray crystallography is a powerful strategy for discovering allosteric ligands for protein targets. Cryocooling of crystals should theoretically increase the fraction of occupied binding sites and decrease radiation damage. However, it might also perturb protein conformations that can be accessed at room temperature. Using data from crystals measured consecutively at room temperature and at cryogenic temperature, we found that transient binding sites could be abolished at the cryogenic temperatures employed by standard approaches. Changing the temperature at which the crystallographic data was collected could provide a deliberate perturbation to the equilibrium of protein conformations and help to visualize hidden sites with great potential to allosterically modulate protein function.
-One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites.,Fischer M, Shoichet BK, Fraser JS Chembiochem. 2015 May 28. doi: 10.1002/cbic.201500196. PMID:26032594<ref>PMID:26032594</ref>
+==See Also==
+*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4xv6" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Baker's yeast]]
+[[Category: Large Structures]]
-[[Category: Cytochrome-c peroxidase]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Fischer, M]]
+[[Category: Fischer M]]
-[[Category: Fraser, J S]]
+[[Category: Fraser JS]]
-[[Category: Cryptic site]]
-[[Category: Flexibility]]
-[[Category: Ligand binding]]
-[[Category: Model system]]
-[[Category: Oxidoreductase]]
-[[Category: Thermodynamic]]
-[[Category: Transient protein site]]