3p5w

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3p5w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinidia_arguta Actinidia arguta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3P5W FirstGlance]. <br>
<table><tr><td colspan='2'>[[3p5w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinidia_arguta Actinidia arguta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3P5W FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1aec|1aec]], [[2act|2act]], [[3p5u|3p5u]], [[3p5v|3p5v]], [[3p5x|3p5x]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Actinidain Actinidain], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.14 3.4.22.14] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3p5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p5w OCA], [https://pdbe.org/3p5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3p5w RCSB], [https://www.ebi.ac.uk/pdbsum/3p5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3p5w ProSAT]</span></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=3p5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p5w OCA], [https://pdbe.org/3p5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3p5w RCSB], [https://www.ebi.ac.uk/pdbsum/3p5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3p5w ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/A5HII2_ACTAR A5HII2_ACTAR]
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The structure of the 24 kDa cysteine protease saru-actinidin from the fruit of Actinidia arguta Planch. (sarunashi) was determined by the cadmium/sulfur-SAD method with X-ray diffraction data collected using in-house Cu Kalpha and Cr Kalpha radiation. The anomalous scatterers included nine sulfurs and several cadmium ions from the crystallization solution. The high quality of the diffraction data, the use of chromium-anode X-ray radiation and the substantial anomalous signal allowed structure determination and automated model building despite both a low solvent content (&lt;40%) and low data multiplicity. The amino-acid sequence of saru-actinidin was deduced from the cDNA and was modified based on experimental electron-density maps at 1.5 A resolution. The active site of saru-actinidin is occupied by a cadmium ion and the active-site cysteine is found to be in an unmodified, cysteine sulfenic acid or cysteine sulfinic acid form. The cadmium sites, coordination geometries and polygonal water structures on the protein surface have also been extensively analyzed. An analysis and comparison of the sulfur/cadmium anomalous signals at the Cu Kalpha and Cr Kalpha wavelengths was carried out. It is proposed that the inclusion of cadmium salts in crystallization solutions coupled with chromium-anode radiation can provide a convenient route for structure determination.
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Structural analysis of actinidin and a comparison of cadmium and sulfur anomalous signals from actinidin crystals measured using in-house copper- and chromium-anode X-ray sources.,Yogavel M, Nithya N, Suzuki A, Sugiyama Y, Yamane T, Velmurugan D, Sharma A Acta Crystallogr D Biol Crystallogr. 2010 Dec;66(Pt 12):1323-33. Epub 2010, Nov 20. PMID:21123873<ref>PMID:21123873</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3p5w" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Actinidain]]
 
[[Category: Actinidia arguta]]
[[Category: Actinidia arguta]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Devadasan, V]]
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[[Category: Devadasan V]]
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[[Category: Manickam, Y]]
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[[Category: Manickam Y]]
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[[Category: Nirmal, N]]
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[[Category: Nirmal N]]
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[[Category: Sharma, A]]
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[[Category: Sharma A]]
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[[Category: Sugiyama, Y]]
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[[Category: Sugiyama Y]]
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[[Category: Suzuki, A]]
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[[Category: Suzuki A]]
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[[Category: Yamane, T]]
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[[Category: Yamane T]]
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[[Category: Cysteine proteinase]]
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[[Category: Hydrolase]]
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[[Category: Sad]]
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Revision as of 11:21, 21 February 2024

Actinidin from Actinidia arguta planch (Sarusashi)

PDB ID 3p5w

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