+Open data
-Basic information
Entry | Database: PDB / ID: 7zqw | ||||||||||||
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Title | Structure of the SARS-CoV-1 main protease in complex with AG7404 | ||||||||||||
Components | 3C-like proteinase nsp5 | ||||||||||||
Keywords | VIRAL PROTEIN / Protease / Inhibitor / SARS-CoV-1 | ||||||||||||
Function / homology | Function and homology information Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral genome replication ...Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral genome replication / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / 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 / 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 / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / proteolysis / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||||||||
Biological species | Severe acute respiratory syndrome coronavirus | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å | ||||||||||||
Authors | Muriel-Goni, S. / Fabrega-Ferrer, M. / Herrera-Morande, A. / Coll, M. | ||||||||||||
Funding support | Spain, 3items
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Citation | Journal: Antiviral Res. / Year: 2022 Title: Structure and inhibition of SARS-CoV-1 and SARS-CoV-2 main proteases by oral antiviral compound AG7404. Authors: Fabrega-Ferrer, M. / Herrera-Morande, A. / Muriel-Goni, S. / Perez-Saavedra, J. / Bueno, P. / Castro, V. / Garaigorta, U. / Gastaminza, P. / Coll, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zqw.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zqw.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 7zqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zqw_validation.pdf.gz | 691.4 KB | Display | wwPDB validaton report |
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Full document | 7zqw_full_validation.pdf.gz | 696.4 KB | Display | |
Data in XML | 7zqw_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 7zqw_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/7zqw ftp://data.pdbj.org/pub/pdb/validation_reports/zq/7zqw | HTTPS FTP |
-Related structure data
Related structure data | 7p35C 7zqvC 1uj1S C: citing same article (ref.) S: Starting model for refinement |
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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: 33876.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus Gene: 1a / Production host: Escherichia coli (E. coli) References: UniProt: P0C6U8, SARS coronavirus main proteinase |
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#2: Chemical | ChemComp-XNV / |
#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: 1.91 Å3/Da / Density % sol: 35.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Lithium Sulfate Monohydrate, HEPES, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→53.55 Å / Num. obs: 7634 / % possible obs: 91.9 % / Redundancy: 4.2 % / CC1/2: 0.998 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.53→2.69 Å / Num. unique obs: 382 / CC1/2: 0.431 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UJ1 Resolution: 2.53→53.55 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 19.133 / SU ML: 0.375 / Cross valid method: THROUGHOUT / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 65.935 Å2
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Refinement step | Cycle: 1 / Resolution: 2.53→53.55 Å
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