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- PDB-7faz: Crystal structure of the SARS-CoV-2 main protease in complex with Y180 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7faz | ||||||
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Title | Crystal structure of the SARS-CoV-2 main protease in complex with Y180 | ||||||
![]() | 3C-like proteinase | ||||||
![]() | VIRAL PROTEIN / coronavirus / protease / inhibitor / complex. | ||||||
Function / homology | ![]() 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 / SARS-CoV-2 modulates host translation machinery / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell Golgi apparatus / methylation / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zeng, R. / Quan, B.X. / Liu, X.L. / Lei, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: An orally available M pro inhibitor is effective against wild-type SARS-CoV-2 and variants including Omicron. Authors: Quan, B.X. / Shuai, H. / Xia, A.J. / Hou, Y. / Zeng, R. / Liu, X.L. / Lin, G.F. / Qiao, J.X. / Li, W.P. / Wang, F.L. / Wang, K. / Zhou, R.J. / Yuen, T.T. / Chen, M.X. / Yoon, C. / Wu, M. / ...Authors: Quan, B.X. / Shuai, H. / Xia, A.J. / Hou, Y. / Zeng, R. / Liu, X.L. / Lin, G.F. / Qiao, J.X. / Li, W.P. / Wang, F.L. / Wang, K. / Zhou, R.J. / Yuen, T.T. / Chen, M.X. / Yoon, C. / Wu, M. / Zhang, S.Y. / Huang, C. / Wang, Y.F. / Yang, W. / Tian, C. / Li, W.M. / Wei, Y.Q. / Yuen, K.Y. / Chan, J.F. / Lei, J. / Chu, H. / Yang, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.7 KB | Display | ![]() |
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PDB format | ![]() | 108 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 40.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7fayC ![]() 7c7pS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33825.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P0DTC1, SARS coronavirus main proteinase #2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium acetate trihydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978516 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→19.9 Å / Num. obs: 40029 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.052 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.1→2.16 Å / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3251 / CC1/2: 0.861 / Rpim(I) all: 0.446 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7C7P Resolution: 2.1→19.9 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.4 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.33 Å2 / Biso mean: 40.6329 Å2 / Biso min: 14.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→19.9 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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