3dyb

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m (Protected "3dyb" [edit=sysop:move=sysop])
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[[Image:3dyb.png|left|200px]]
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==proteinase K- digalacturonic acid complex==
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<StructureSection load='3dyb' size='340' side='right' caption='[[3dyb]], [[Resolution|resolution]] 1.32&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3dyb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Engyodontium_album Engyodontium album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DYB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DYB 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=AD0:DIGALACTURONIC+ACID'>AD0</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></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/Peptidase_K Peptidase K], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.64 3.4.21.64] </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=3dyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dyb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dyb RCSB], [http://www.ebi.ac.uk/pdbsum/3dyb PDBsum]</span></td></tr>
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</table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dy/3dyb_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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/chain_selection.php?pdb_ID=2ata ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Proteinase K, a subtilisin-like fungal protease, was crystallized from a cocktail of small molecules containing digalacturonic acid (DGA). The crystal structure was determined to 1.32 A resolution and refined to an R factor of 0.158. The final model contained, beside the protein, two calcium ions, 379 water molecules, a molecule of DGA and a partially occupied HEPES molecule. The DGA molecule has one sugar moiety disposed exactly on a crystallographic twofold axis; the second ring was not observed. The DGA molecule is bound to two protein molecules across the twofold axis through hydrogen-bonding networks involving Ser150 and water molecules. One of the calcium-ion sites has not been reported previously. This study further illustrates the involvement of small molecules in the crystallization of macromolecules through their ability to form intermolecular lattice interactions.
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{{STRUCTURE_3dyb| PDB=3dyb | SCENE= }}
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High-resolution structure of proteinase K cocrystallized with digalacturonic acid.,Larson SB, Day JS, Nguyen C, Cudney R, McPherson A Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Mar 1;65(Pt, 3):192-8. Epub 2009 Feb 12. PMID:19255463<ref>PMID:19255463</ref>
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===proteinase K- digalacturonic acid complex===
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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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{{ABSTRACT_PUBMED_19255463}}
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==See Also==
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*[[Proteinase|Proteinase]]
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==About this Structure==
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== References ==
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[[3dyb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Engyodontium_album Engyodontium album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DYB OCA].
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<references/>
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__TOC__
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==Reference==
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</StructureSection>
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<ref group="xtra">PMID:019255463</ref><references group="xtra"/>
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[[Category: Engyodontium album]]
[[Category: Engyodontium album]]
[[Category: Peptidase K]]
[[Category: Peptidase K]]
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[[Category: CHTSB, Center for High-Throughput Structural Biology.]]
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[[Category: CHTSB, Center for High-Throughput Structural Biology]]
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[[Category: Cudney, R.]]
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[[Category: Cudney, R]]
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[[Category: Day, J S.]]
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[[Category: Day, J S]]
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[[Category: Larson, S B.]]
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[[Category: Larson, S B]]
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[[Category: McPherson, A.]]
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[[Category: McPherson, A]]
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[[Category: Nguyen, C.]]
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[[Category: Nguyen, C]]
[[Category: Center for high-throughput structural biology]]
[[Category: Center for high-throughput structural biology]]
[[Category: Chtsb]]
[[Category: Chtsb]]
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[[Category: Porteinase k]]
[[Category: Porteinase k]]
[[Category: Protease]]
[[Category: Protease]]
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[[Category: Protein structure initiative]]
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[[Category: PSI, Protein structure initiative]]
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[[Category: Psi-2]]
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[[Category: Serine protease]]
[[Category: Serine protease]]
[[Category: Silverbullet]]
[[Category: Silverbullet]]
[[Category: Structural genomic]]
[[Category: Structural genomic]]
[[Category: Zymogen]]
[[Category: Zymogen]]

Revision as of 13:22, 19 November 2014

proteinase K- digalacturonic acid complex

3dyb, resolution 1.32Å

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