+Open data
-Basic information
Entry | Database: PDB / ID: 8ifr | ||||||
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Title | SARS-CoV-2 3CL protease (3CLpro) in complex with compound 3 | ||||||
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 / 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 / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / ubiquitinyl hydrolase 1 / methylation / 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 / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral translational frameshifting / 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: 1.66 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: Nat Commun / Year: 2023 Title: Structure-based development and preclinical evaluation of the SARS-CoV-2 3C-like protease inhibitor simnotrelvir. Authors: Jiang, X. / Su, H. / Shang, W. / Zhou, F. / Zhang, Y. / Zhao, W. / Zhang, Q. / Xie, H. / Jiang, L. / Nie, T. / Yang, F. / Xiong, M. / Huang, X. / Li, M. / Chen, P. / Peng, S. / Xiao, G. / ...Authors: Jiang, X. / Su, H. / Shang, W. / Zhou, F. / Zhang, Y. / Zhao, W. / Zhang, Q. / Xie, H. / Jiang, L. / Nie, T. / Yang, F. / Xiong, M. / Huang, X. / Li, M. / Chen, P. / Peng, S. / Xiao, G. / Jiang, H. / Tang, R. / Zhang, L. / Shen, J. / Xu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ifr.cif.gz | 137.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ifr.ent.gz | 106 KB | Display | PDB format |
PDBx/mmJSON format | 8ifr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ifr_validation.pdf.gz | 793.2 KB | Display | wwPDB validaton report |
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Full document | 8ifr_full_validation.pdf.gz | 793.2 KB | Display | |
Data in XML | 8ifr_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 8ifr_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/8ifr ftp://data.pdbj.org/pub/pdb/validation_reports/if/8ifr | HTTPS FTP |
-Related structure data
Related structure data | 8ifpC 8ifqC 8ifsC 8iftC 8igxC 8igyC 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) / Strain (production host): BL21(DE3) References: UniProt: P0DTC1, SARS coronavirus main proteinase |
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#2: Chemical | ChemComp-P0O / ( |
#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: 45.68 % |
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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: BL02U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 20, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→54.54 Å / Num. obs: 36606 / % possible obs: 99.1 % / Redundancy: 9.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.046 / Rrim(I) all: 0.14 / Χ2: 0.94 / Net I/σ(I): 13.2 / Num. measured all: 342897 |
Reflection shell | Resolution: 1.66→1.75 Å / % possible obs: 97.8 % / Redundancy: 9.9 % / Rmerge(I) obs: 1.367 / Num. measured all: 51192 / Num. unique obs: 5186 / CC1/2: 0.635 / Rpim(I) all: 0.46 / Rrim(I) all: 1.444 / Χ2: 0.86 / Net I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→30.79 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.39 / 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: 1.66→30.79 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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