4xva: Difference between revisions

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<StructureSection load='4xva' size='340' side='right'caption='[[4xva]], [[Resolution|resolution]] 2.66&Aring;' scene=''>
<StructureSection load='4xva' size='340' side='right'caption='[[4xva]], [[Resolution|resolution]] 2.66&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4xva]] is a 4 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=4XVA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XVA FirstGlance]. <br>
<table><tr><td colspan='2'>[[4xva]] is a 4 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=4XVA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XVA FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BZI:BENZIMIDAZOLE'>BZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 2.66&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xv4|4xv4]], [[4xv5|4xv5]], [[4xv6|4xv6]], [[4xv7|4xv7]], [[4xv8|4xv8]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BZI:BENZIMIDAZOLE'>BZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=4xva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xva OCA], [https://pdbe.org/4xva PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xva RCSB], [https://www.ebi.ac.uk/pdbsum/4xva PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xva 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=4xva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xva OCA], [http://pdbe.org/4xva PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xva RCSB], [http://www.ebi.ac.uk/pdbsum/4xva PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xva ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== 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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4xva" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Baker's yeast]]
[[Category: Cytochrome-c peroxidase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Fischer, M]]
[[Category: Saccharomyces cerevisiae S288C]]
[[Category: Fraser, J S]]
[[Category: Fischer M]]
[[Category: Cryptic site]]
[[Category: Fraser JS]]
[[Category: Flexibility]]
[[Category: Ligand binding]]
[[Category: Model system]]
[[Category: Oxidoreductase]]
[[Category: Thermodynamic]]
[[Category: Transient protein site]]

Latest revision as of 16:01, 1 March 2024

Crystal structure of wild type cytochrome c peroxidaseCrystal structure of wild type cytochrome c peroxidase

Structural highlights

4xva is a 4 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.66Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CCPR_YEAST Destroys radicals which are normally produced within the cells and which are toxic to biological systems.

See Also

4xva, resolution 2.66Å

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