7q9c: Difference between revisions
New page: '''Unreleased structure''' The entry 7q9c is ON HOLD Authors: Loboda, J., Sosnowski, P., Tusar, L., Vidmar, R., Vizovisek, M., Horvat, J., Kosec, G., Impens, F., Demol, H., Turk, B., Ge... |
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==Peptide RLSAKP in complex with human cathepsin V C25A mutant== | |||
<StructureSection load='7q9c' size='340' side='right'caption='[[7q9c]], [[Resolution|resolution]] 1.40Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7q9c]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Q9C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Q9C FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=TFA:TRIFLUOROACETIC+ACID'>TFA</scene></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=7q9c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7q9c OCA], [https://pdbe.org/7q9c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7q9c RCSB], [https://www.ebi.ac.uk/pdbsum/7q9c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7q9c ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Addressing the elusive specificity of cysteine cathepsins, which in contrast to caspases and trypsin-like proteases lack strict specificity determining P1 pocket, calls for innovative approaches. Proteomic analysis of cell lysates with human cathepsins K, V, B, L, S, and F identified 30,000 cleavage sites, which we analyzed by software platform SAPS-ESI (Statistical Approach to Peptidyl Substrate-Enzyme Specific Interactions). SAPS-ESI is used to generate clusters and training sets for support vector machine learning. Cleavage site predictions on the SARS-CoV-2 S protein, confirmed experimentally, expose the most probable first cut under physiological conditions and suggested furin-like behavior of cathepsins. Crystal structure analysis of representative peptides in complex with cathepsin V reveals rigid and flexible sites consistent with analysis of proteomics data by SAPS-ESI that correspond to positions with heterogeneous and homogeneous distribution of residues. Thereby support for design of selective cleavable linkers of drug conjugates and drug discovery studies is provided. | |||
Proteomic data and structure analysis combined reveal interplay of structural rigidity and flexibility on selectivity of cysteine cathepsins.,Tusar L, Loboda J, Impens F, Sosnowski P, Van Quickelberghe E, Vidmar R, Demol H, Sedeyn K, Saelens X, Vizovisek M, Mihelic M, Fonovic M, Horvat J, Kosec G, Turk B, Gevaert K, Turk D Commun Biol. 2023 Apr 24;6(1):450. doi: 10.1038/s42003-023-04772-8. PMID:37095140<ref>PMID:37095140</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Demol | <div class="pdbe-citations 7q9c" style="background-color:#fffaf0;"></div> | ||
[[Category: Gevaert | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Homo sapiens]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Turk | [[Category: Demol H]] | ||
[[Category: Turk | [[Category: Gevaert K]] | ||
[[Category: | [[Category: Horvat J]] | ||
[[Category: | [[Category: Impens F]] | ||
[[Category: | [[Category: Kosec G]] | ||
[[Category: Loboda J]] | |||
[[Category: Sosnowski P]] | |||
[[Category: Turk B]] | |||
[[Category: Turk D]] | |||
[[Category: Tusar L]] | |||
[[Category: Vidmar R]] | |||
[[Category: Vizovisek M]] | |||