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Yorodumi- PDB-7mng: Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) in Co... -
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-Basic information
Entry | Database: PDB / ID: 7mng | |||||||||||||||
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Title | Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) in Complex with Covalent Inhibitor VBY-825 (Partial Occupancy) | |||||||||||||||
Components | 3C-like proteinase | |||||||||||||||
Keywords | VIRAL PROTEIN / HYDROLASE/INHIBITOR / SARS-CoV-2 / Main Protease / 3CLpro/Mpro / VBY-825 / Inhibitor / HYDROLASE-INHIBITOR COMPLEX | |||||||||||||||
Function / homology | Function and homology information protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / snRNP Assembly / Replication of the SARS-CoV-2 genome / TRAF3-dependent IRF activation pathway / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / : / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / 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 / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / DNA helicase / 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 / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / copper ion binding / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 / identical protein binding Similarity search - Function | |||||||||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||||||||
Authors | Andi, B. / Kumaran, D. / Soares, A.S. / Kreitler, D.F. / Shi, W. / Jakoncic, J. / Fuchs, M.R. / Keereetaweep, J. / Shanklin, J. / McSweeney, S. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Sci Rep / Year: 2022 Title: Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease. Authors: Andi, B. / Kumaran, D. / Kreitler, D.F. / Soares, A.S. / Keereetaweep, J. / Jakoncic, J. / Lazo, E.O. / Shi, W. / Fuchs, M.R. / Sweet, R.M. / Shanklin, J. / Adams, P.D. / Schmidt, J.G. / ...Authors: Andi, B. / Kumaran, D. / Kreitler, D.F. / Soares, A.S. / Keereetaweep, J. / Jakoncic, J. / Lazo, E.O. / Shi, W. / Fuchs, M.R. / Sweet, R.M. / Shanklin, J. / Adams, P.D. / Schmidt, J.G. / Head, M.S. / McSweeney, S. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mng.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mng.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 7mng.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/7mng ftp://data.pdbj.org/pub/pdb/validation_reports/mn/7mng | HTTPS FTP |
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-Related structure data
Related structure data | 7jycC 7k3tC 7k40SC 7k6dC 7k6eC 7mrrC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33825.547 Da / Num. of mol.: 1 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, SARS coronavirus main proteinase | ||||
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#2: Chemical | ChemComp-ZL7 / ( | ||||
#3: Chemical | ChemComp-DMS / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.25 % / Description: Very thin small plate |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 4000, HEPES pH 7.0, 1 mM VBY-825 (in final drop), 4% DMSO (in final drop) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2021 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→28.14 Å / Num. obs: 29633 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.059 / Rrim(I) all: 0.194 / Net I/σ(I): 9 / Num. measured all: 305100 / Scaling rejects: 644 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7K40 Resolution: 1.7→28.16 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.2182 / WRfactor Rwork: 0.1779 / FOM work R set: 0.835 / SU R Cruickshank DPI: 0.1288 / SU Rfree: 0.1204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.12 / 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: 139.95 Å2 / Biso mean: 26.133 Å2 / Biso min: 13.04 Å2
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Refinement step | Cycle: final / Resolution: 1.7→28.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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