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- PDB-6xa9: SARS CoV-2 PLpro in complex with ISG15 C-terminal domain propargy... -
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Basic information
Entry | Database: PDB / ID: 6xa9 | |||||||||
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Title | SARS CoV-2 PLpro in complex with ISG15 C-terminal domain propargylamide | |||||||||
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![]() | HYDROLASE/SUBSTRATE / SARS CoV-2 / papain-like protease / ISG15CTD activity based probe / COVID19 / HYDROLASE-SUBSTRATE complex | |||||||||
Function / homology | ![]() positive regulation of protein oligomerization / ISG15-protein conjugation / regulation of type II interferon production / protein localization to mitochondrion / NS1 Mediated Effects on Host Pathways / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / RSV-host interactions / positive regulation of interleukin-10 production ...positive regulation of protein oligomerization / ISG15-protein conjugation / regulation of type II interferon production / protein localization to mitochondrion / NS1 Mediated Effects on Host Pathways / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / RSV-host interactions / positive regulation of interleukin-10 production / polyubiquitin modification-dependent protein binding / positive regulation of bone mineralization / negative regulation of protein ubiquitination / positive regulation of interferon-beta production / positive regulation of erythrocyte differentiation / Negative regulators of DDX58/IFIH1 signaling / integrin-mediated signaling pathway / Termination of translesion DNA synthesis / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / PKR-mediated signaling / ISG15 antiviral mechanism / modification-dependent protein catabolic process / protein tag activity / Interferon alpha/beta signaling / positive regulation of type II interferon production / integrin binding / protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / ubiquitin-dependent protein catabolic process / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / defense response to virus / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / defense response to bacterium / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / innate immune response / virus-mediated perturbation of host defense response / DNA-templated transcription / lipid binding / ubiquitin protein ligase binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / extracellular region / nucleoplasm / ATP binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Klemm, T. / Calleja, D.J. / Richardson, L.W. / Lechtenberg, B.C. / Komander, D. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2. Authors: Klemm, T. / Ebert, G. / Calleja, D.J. / Allison, C.C. / Richardson, L.W. / Bernardini, J.P. / Lu, B.G. / Kuchel, N.W. / Grohmann, C. / Shibata, Y. / Gan, Z.Y. / Cooney, J.P. / Doerflinger, M. ...Authors: Klemm, T. / Ebert, G. / Calleja, D.J. / Allison, C.C. / Richardson, L.W. / Bernardini, J.P. / Lu, B.G. / Kuchel, N.W. / Grohmann, C. / Shibata, Y. / Gan, Z.Y. / Cooney, J.P. / Doerflinger, M. / Au, A.E. / Blackmore, T.R. / van der Heden van Noort, G.J. / Geurink, P.P. / Ovaa, H. / Newman, J. / Riboldi-Tunnicliffe, A. / Czabotar, P.E. / Mitchell, J.P. / Feltham, R. / Lechtenberg, B.C. / Lowes, K.N. / Dewson, G. / Pellegrini, M. / Lessene, G. / Komander, D. #1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution. Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart / ![]() Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms. | |||||||||
History |
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-Validation report
Summary document | ![]() | 484.1 KB | Display | ![]() |
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Full document | ![]() | 496.3 KB | Display | |
Data in XML | ![]() | 40.8 KB | Display | |
Data in CIF | ![]() | 55.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xaaC ![]() 6ffaS ![]() 6wrhS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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