+Open data
-Basic information
Entry | Database: PDB / ID: 8igy | ||||||
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Title | SARS-CoV-2 3CL protease (3CLpro) in complex with nirmatrelvir | ||||||
Components | 3C-like proteinase nsp5 | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / Mpro / 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: 1.96 Å | ||||||
Authors | Su, H.X. / Zhao, W.F. / Xie, H. / Nie, T.Q. / Li, M.J. / Xu, Y.C. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Discovery of oral simnotrelvir, an approved SARS-CoV-2 3C-like protease inhibitor for the treatment of COVID-19 Authors: Jiang, X. / Su, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8igy.cif.gz | 130.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8igy.ent.gz | 99.4 KB | Display | PDB format |
PDBx/mmJSON format | 8igy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/8igy ftp://data.pdbj.org/pub/pdb/validation_reports/ig/8igy | HTTPS FTP |
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-Related structure data
Related structure data | 8ifpC 8ifqC 8ifrC 8ifsC 8iftC 8igxC 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: 33825.547 Da / Num. of mol.: 1 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, SARS coronavirus main proteinase |
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#2: Chemical | ChemComp-4WI / ( |
#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: 2.26 Å3/Da / Density % sol: 45.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES, pH5.5-6.5, 10%-25% PEG6000, 3% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→105.28 Å / Num. obs: 21107 / % possible obs: 92.2 % / Redundancy: 9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.039 / Rrim(I) all: 0.121 / Χ2: 0.96 / Net I/σ(I): 15.1 / Num. measured all: 190561 |
Reflection shell | Resolution: 1.96→2.06 Å / % possible obs: 93.1 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.831 / Num. measured all: 23834 / Num. unique obs: 3063 / CC1/2: 0.798 / Rpim(I) all: 0.309 / Rrim(I) all: 0.888 / Χ2: 0.91 / Net I/σ(I) obs: 2.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→27.81 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→27.81 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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