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- PDB-7ntq: Crystal structure of the SARS-CoV-2 Main Protease complexed with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ntq | ||||||
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Title | Crystal structure of the SARS-CoV-2 Main Protease complexed with N-(pyridin-3-ylmethyl)thioformamide | ||||||
![]() | 3C-like proteinase | ||||||
![]() | VIRAL PROTEIN / 3CLpro / main protease / SARS-CoV-2 / 2019-nCov / inhibitor | ||||||
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 / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dupre, E. / Villeret, V. / Hanoulle, X. | ||||||
![]() | ![]() Title: Novel dithiocarbamates selectively inhibit 3CL protease of SARS-CoV-2 and other coronaviruses. Authors: Brier, L. / Hassan, H. / Hanoulle, X. / Landry, V. / Moschidi, D. / Desmarets, L. / Rouille, Y. / Dumont, J. / Herledan, A. / Warenghem, S. / Piveteau, C. / Carre, P. / Ikherbane, S. / ...Authors: Brier, L. / Hassan, H. / Hanoulle, X. / Landry, V. / Moschidi, D. / Desmarets, L. / Rouille, Y. / Dumont, J. / Herledan, A. / Warenghem, S. / Piveteau, C. / Carre, P. / Ikherbane, S. / Cantrelle, F.X. / Dupre, E. / Dubuisson, J. / Belouzard, S. / Leroux, F. / Deprez, B. / Charton, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.9 KB | Display | ![]() |
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PDB format | ![]() | 101.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 720.2 KB | Display | ![]() |
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Full document | ![]() | 720.3 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8aebC ![]() 7k3tS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33825.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pHisSUMO / Production host: ![]() ![]() References: UniProt: P0DTC1, SARS coronavirus main proteinase |
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-Non-polymers , 5 types, 232 molecules ![](data/chem/img/35J.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-35J / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-FMT / #5: Chemical | ChemComp-DMS / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M NaFormate, 20% PEG 3350, 10% Glycerol, 10% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978564 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→47.84 Å / Num. obs: 42066 / % possible obs: 98.7 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 9.77 |
Reflection shell | Resolution: 1.49→1.59 Å / Num. unique obs: 6311 / CC1/2: 0.51 / % possible all: 91.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7K3T Resolution: 1.495→43.809 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.002 / SU ML: 0.07 / Cross valid method: FREE R-VALUE / ESU R: 0.075 / ESU R Free: 0.084 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.691 Å2
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Refinement step | Cycle: LAST / Resolution: 1.495→43.809 Å
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Refine LS restraints |
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LS refinement shell |
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