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Yorodumi- PDB-6ywk: Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in co... -
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Basic information
| Entry | Database: PDB / ID: 6ywk | ||||||
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| Title | Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with HEPES | ||||||
Components | NSP3 macrodomain | ||||||
Keywords | VIRAL PROTEIN / NSP3 / macrodomain / ADP-ribose-1"-phosphatase / ADRP / Covid-19 / SARS-COV-2 / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
| Function / homology | Function and homology informationprotein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ni, X. / Schroeder, M. / Olieric, V. / Sharpe, E.M. / Wojdyla, J.A. / Wang, M. / Knapp, S. / Chaikuad, A. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2021Title: Structural Insights into Plasticity and Discovery of Remdesivir Metabolite GS-441524 Binding in SARS-CoV-2 Macrodomain. Authors: Ni, X. / Schroder, M. / Olieric, V. / Sharpe, M.E. / Hernandez-Olmos, V. / Proschak, E. / Merk, D. / Knapp, S. / Chaikuad, A. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 6ywk.cif.gz | 335.8 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb6ywk.ent.gz | 275.7 KB | Display | PDB format |
| PDBx/mmJSON format | 6ywk.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 6ywk_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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| Full document | 6ywk_full_validation.pdf.gz | 1.1 MB | Display | |
| Data in XML | 6ywk_validation.xml.gz | 35.4 KB | Display | |
| Data in CIF | 6ywk_validation.cif.gz | 50.1 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/6ywk ftp://data.pdbj.org/pub/pdb/validation_reports/yw/6ywk | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 6ywlC ![]() 6ywmC ![]() 7bf3C ![]() 7bf4C ![]() 7bf5C ![]() 7bf6C ![]() 6wenS 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: Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: _
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