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3p5u

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==Actinidin from Actinidia arguta planch (Sarusashi)==
==Actinidin from Actinidia arguta planch (Sarusashi)==
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<StructureSection load='3p5u' size='340' side='right' caption='[[3p5u]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
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<StructureSection load='3p5u' size='340' side='right'caption='[[3p5u]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3p5u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Actinidia_arguta Actinidia arguta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P5U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3P5U FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3p5u]] 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=3P5U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3P5U FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 1.5&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></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>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1aec|1aec]], [[2act|2act]], [[3p5v|3p5v]], [[3p5w|3p5w]], [[3p5x|3p5x]]</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=3p5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p5u OCA], [https://pdbe.org/3p5u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3p5u RCSB], [https://www.ebi.ac.uk/pdbsum/3p5u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3p5u ProSAT]</span></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Actinidain Actinidain], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3p5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p5u OCA], [http://pdbe.org/3p5u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3p5u RCSB], [http://www.ebi.ac.uk/pdbsum/3p5u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3p5u ProSAT]</span></td></tr>
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</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 3p5u" 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]]
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[[Category: Devadasan, V]]
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[[Category: Large Structures]]
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[[Category: Manickam, Y]]
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[[Category: Devadasan V]]
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[[Category: Nirmal, N]]
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[[Category: Manickam Y]]
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[[Category: Sharma, A]]
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[[Category: Nirmal N]]
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[[Category: Sugiyama, Y]]
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[[Category: Sharma A]]
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[[Category: Suzuki, A]]
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[[Category: Sugiyama Y]]
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[[Category: Yamane, T]]
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[[Category: Suzuki A]]
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[[Category: Cysteine proteinase]]
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[[Category: Yamane T]]
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[[Category: Hydrolase]]
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[[Category: Sad]]
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Current revision

Actinidin from Actinidia arguta planch (Sarusashi)

PDB ID 3p5u

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