3sdk

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==Structure of yeast 20S open-gate proteasome with Compound 34==
==Structure of yeast 20S open-gate proteasome with Compound 34==
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<StructureSection load='3sdk' size='340' side='right' caption='[[3sdk]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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<StructureSection load='3sdk' size='340' side='right'caption='[[3sdk]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3sdk]] is a 28 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SDK FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3sdk]] is a 20 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=3SDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SDK 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=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=P3N:N-[(2S)-3-(3-TERT-BUTYL-1,2,4-OXADIAZOL-5-YL)-1-({(2S)-1-[(4-METHYLBENZYL)AMINO]-1-OXO-4-PHENYLBUTAN-2-YL}AMINO)-1-OXOPROPAN-2-YL]-5-METHYL-1,2-OXAZOLE-3-CARBOXAMIDE'>P3N</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]] 2.7&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3mg4|3mg4]], [[3mg6|3mg6]], [[3mg7|3mg7]], [[3mg8|3mg8]], [[3oeu|3oeu]], [[3oev|3oev]], [[3sdi|3sdi]]</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=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=P3N:N-[(2S)-3-(3-TERT-BUTYL-1,2,4-OXADIAZOL-5-YL)-1-({(2S)-1-[(4-METHYLBENZYL)AMINO]-1-OXO-4-PHENYLBUTAN-2-YL}AMINO)-1-OXOPROPAN-2-YL]-5-METHYL-1,2-OXAZOLE-3-CARBOXAMIDE'>P3N</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/Proteasome_endopeptidase_complex Proteasome endopeptidase complex], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.25.1 3.4.25.1] </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=3sdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sdk OCA], [https://pdbe.org/3sdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sdk RCSB], [https://www.ebi.ac.uk/pdbsum/3sdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sdk ProSAT]</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=3sdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sdk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sdk RCSB], [http://www.ebi.ac.uk/pdbsum/3sdk PDBsum]</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/PSA6_YEAST PSA6_YEAST] The proteasome degrades poly-ubiquitinated proteins in the cytoplasm and in the nucleus. It is essential for the regulated turnover of proteins and for the removal of misfolded proteins. The proteasome is a multicatalytic proteinase complex that is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. It has an ATP-dependent proteolytic activity.
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Starting from a tripeptide screening hit, a series of dipeptide inhibitors of the proteasome with Thr as the P3 residue has been optimized with the aid of crystal structures in complex with the beta-5/6 active site of y20S. Derivative 25, (beta5 IC(50)=7.4 nM) inhibits only the chymotryptic activity of the proteasome, shows cellular activity against targets in the UPS, and inhibits proliferation.
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Optimization of a series of dipeptides with a P3 threonine residue as non-covalent inhibitors of the chymotrypsin-like activity of the human 20S proteasome.,Blackburn C, Barrett C, Blank JL, Bruzzese FJ, Bump N, Dick LR, Fleming P, Garcia K, Hales P, Hu Z, Jones M, Liu JX, Sappal DS, Sintchak MD, Tsu C, Gigstad KM Bioorg Med Chem Lett. 2010 Nov 15;20(22):6581-6. Epub 2010 Sep 15. PMID:20875739<ref>PMID:20875739</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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==See Also==
==See Also==
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*[[Proteasome|Proteasome]]
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*[[Proteasome 3D structures|Proteasome 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Proteasome endopeptidase complex]]
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[[Category: Large Structures]]
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[[Category: Saccharomyces cerevisiae]]
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[[Category: Saccharomyces cerevisiae S288C]]
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[[Category: Sintchak, M D]]
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[[Category: Sintchak MD]]
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[[Category: 20s proteasome]]
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[[Category: Hydrolase-hydrolase inhibitor complex]]
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Current revision

Structure of yeast 20S open-gate proteasome with Compound 34

PDB ID 3sdk

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OCA

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