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Yorodumi- PDB-7vth: The crystal structure of SARS-CoV-2 3CL protease in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 7vth | ||||||
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Title | The crystal structure of SARS-CoV-2 3CL protease in complex with compound 1 | ||||||
Components | 3C-like proteinase | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / VIRAL PROTEIN-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information viral genome replication / methyltransferase 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 / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase ...viral genome replication / methyltransferase 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 / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / 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 / methylation / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / lipid binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Yamamoto, S. / Tachibana, Y. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Discovery of S-217622, a Noncovalent Oral SARS-CoV-2 3CL Protease Inhibitor Clinical Candidate for Treating COVID-19. Authors: Unoh, Y. / Uehara, S. / Nakahara, K. / Nobori, H. / Yamatsu, Y. / Yamamoto, S. / Maruyama, Y. / Taoda, Y. / Kasamatsu, K. / Suto, T. / Kouki, K. / Nakahashi, A. / Kawashima, S. / Sanaki, T. ...Authors: Unoh, Y. / Uehara, S. / Nakahara, K. / Nobori, H. / Yamatsu, Y. / Yamamoto, S. / Maruyama, Y. / Taoda, Y. / Kasamatsu, K. / Suto, T. / Kouki, K. / Nakahashi, A. / Kawashima, S. / Sanaki, T. / Toba, S. / Uemura, K. / Mizutare, T. / Ando, S. / Sasaki, M. / Orba, Y. / Sawa, H. / Sato, A. / Sato, T. / Kato, T. / Tachibana, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vth.cif.gz | 132 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vth.ent.gz | 99.5 KB | Display | PDB format |
PDBx/mmJSON format | 7vth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vth_validation.pdf.gz | 967.3 KB | Display | wwPDB validaton report |
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Full document | 7vth_full_validation.pdf.gz | 975.1 KB | Display | |
Data in XML | 7vth_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 7vth_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/7vth ftp://data.pdbj.org/pub/pdb/validation_reports/vt/7vth | HTTPS FTP |
-Related structure data
Related structure data | 7vu6C 6y2eS S: Starting model for refinement 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: 34423.340 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli (E. coli) References: UniProt: P0DTC1, SARS coronavirus main proteinase #2: Chemical | #3: 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: 1.98 Å3/Da / Density % sol: 37.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium citrate tribasic pH 7.0, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54178 Å | |||||||||||||||||||||||||||
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 30, 2020 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2→112.95 Å / Num. obs: 36330 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.055 / Rrim(I) all: 0.106 / Net I/σ(I): 8.6 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 2.6 %
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.496
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6y2e Resolution: 2→112.95 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.2485 / WRfactor Rwork: 0.1988 / FOM work R set: 0.8137 / SU B: 5.527 / SU ML: 0.152 / SU R Cruickshank DPI: 0.2318 / SU Rfree: 0.1947 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.31 Å2 / Biso mean: 18.554 Å2 / Biso min: 6.32 Å2
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Refinement step | Cycle: final / Resolution: 2→112.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.053 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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