+Open data
-Basic information
Entry | Database: PDB / ID: 7xq6 | ||||||
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Title | The complex structure of mutant Mpro with inhibitor | ||||||
Components | 3C-like proteinase nsp5 | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / Protease / Cov-2 / 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 / methylation / double membrane vesicle viral factory outer membrane ...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 / methylation / 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 / 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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / symbiont-mediated suppression of host gene expression / cysteine-type endopeptidase activity / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sahoo, P. / Lenka, D.R. / Kumar, A. | ||||||
Funding support | India, 1items
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Citation | Journal: Acs Pharmacol Transl Sci / Year: 2023 Title: Detailed Insights into the Inhibitory Mechanism of New Ebselen Derivatives against Main Protease (M pro ) of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Authors: Sahoo, P. / Lenka, D.R. / Batabyal, M. / Pain, P.K. / Kumar, S. / Manna, D. / Kumar, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xq6.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xq6.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 7xq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/7xq6 ftp://data.pdbj.org/pub/pdb/validation_reports/xq/7xq6 | HTTPS FTP |
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-Related structure data
Related structure data | 7w9gSC 7xq7C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 33888.578 Da / Num. of mol.: 1 / Mutation: H41N 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 |
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#2: Chemical | ChemComp-CL / |
#3: 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: 2.05 Å3/Da / Density % sol: 39.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: Ammonium chloride, MES pH6.5, PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9778 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 27, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 2→34.19 Å / Num. obs: 18139 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.16 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique obs: 1358 / CC1/2: 0.958 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7W9G Resolution: 2→30.59 Å / SU ML: 0.2019 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.3778 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.79 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30.59 Å
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Refine LS restraints |
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LS refinement shell |
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