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Yorodumi- PDB-7xrs: Crystal structure of SARS-Cov-2 main protease in complex with inh... -
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-Basic information
Entry | Database: PDB / ID: 7xrs | ||||||
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Title | Crystal structure of SARS-Cov-2 main protease in complex with inhibitor YH-53 | ||||||
Components | Replicase polyprotein 1a | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Zhou, X.L. / Zhong, F.L. / Lin, C. / Zeng, P. / Zhang, J. / Li, J. | ||||||
Funding support | 1items
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Citation | Journal: Viruses / Year: 2022 Title: Structural Basis for the Inhibition of Coronaviral Main Proteases by a Benzothiazole-Based Inhibitor. Authors: Hu, X. / Lin, C. / Xu, Q. / Zhou, X. / Zeng, P. / McCormick, P.J. / Jiang, H. / Li, J. / Zhang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xrs.cif.gz | 129.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xrs.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 7xrs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xrs_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7xrs_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7xrs_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 7xrs_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/7xrs ftp://data.pdbj.org/pub/pdb/validation_reports/xr/7xrs | HTTPS FTP |
-Related structure data
Related structure data | 7xryC 7ygqC 7c2qS 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: 33148.832 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 BL21(DE3) (bacteria) / References: UniProt: P0DTC1 #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: 2.38 Å3/Da / Density % sol: 48.28 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES 7.5, 20% PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 12, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→52.86 Å / Num. obs: 46180 / % possible obs: 98.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 28.7934372147 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.93→2.03 Å / Rmerge(I) obs: 0.494 / Num. unique obs: 6307 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7C2Q Resolution: 1.93→52.86 Å / SU ML: 0.255415689336 / Cross valid method: FREE R-VALUE / σ(F): 1.33933280431 / Phase error: 27.2445608394 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: 33.9327775583 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→52.86 Å
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Refine LS restraints |
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LS refinement shell |
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