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Yorodumi- PDB-8rjz: Crystal structure of SARS-CoV-2 main protease (MPro) in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rjz | ||||||||||||
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Title | Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the non-covalent inhibitor GUE-3801 (compound 80 in publication) | ||||||||||||
Components | 3C-like proteinase nsp5 | ||||||||||||
Keywords | VIRAL PROTEIN / MPro / main protease / inhibitor | ||||||||||||
Function / homology | Function and homology information 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 ...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 / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / 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 / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / 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 perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent 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 | Severe acute respiratory syndrome coronavirus 2 | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||||||||
Authors | Strater, N. / Claff, T. / Sylvester, K. / Mueller, C.E. / Guetschow, M. / Useini, A. | ||||||||||||
Funding support | Germany, 3items
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Citation | Journal: J.Med.Chem. / Year: 2024 Title: Macrocyclic Azapeptide Nitriles: Structure-Based Discovery of Potent SARS-CoV-2 Main Protease Inhibitors as Antiviral Drugs. Authors: Breidenbach, J. / Voget, R. / Si, Y. / Hingst, A. / Claff, T. / Sylvester, K. / Wolf, V. / Krasniqi, V. / Useini, A. / Strater, N. / Ogura, Y. / Kawaguchi, A. / Muller, C.E. / Gutschow, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rjz.cif.gz | 237 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rjz.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8rjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rjz_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8rjz_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8rjz_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 8rjz_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/8rjz ftp://data.pdbj.org/pub/pdb/validation_reports/rj/8rjz | HTTPS FTP |
-Related structure data
Related structure data | 8rjvC 8rjyC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33825.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli) / References: UniProt: P0DTD1 #2: Chemical | Mass: 587.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H29Cl2FN4O4 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.2 M sodium nitrate, 0.1 M Bis-Tris propane pH 6.5, 20% PEG 3350, 0.4 mM inhibitor |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→66.92 Å / Num. obs: 42154 / % possible obs: 94.4 % / Redundancy: 13.5 % / Biso Wilson estimate: 21.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.047 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.7→1.9 Å / Redundancy: 13.9 % / Rmerge(I) obs: 1.585 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2108 / CC1/2: 0.597 / Rpim(I) all: 0.44 / % possible all: 70.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→66.92 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.26 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→66.92 Å
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Refine LS restraints |
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LS refinement shell |
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