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- PDB-7mlf: Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) Coval... -
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Basic information
Entry | Database: PDB / ID: 7mlf | ||||||
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Title | Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) Covalently Bound to Compound C7 | ||||||
![]() | 3C-like proteinase | ||||||
![]() | HYDROLASE/INHIBITOR / SARS-CoV-2 / 3CLpro / covalent inhibitor / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 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 ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 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 / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / mRNA 5'-cap (guanine-N7-)-methyltransferase 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 / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sharon, I. / Stille, J. / Tjutrins, J. / Wang, G. / Venegas, F.A. / Hennecker, C. / Rueda, A.M. / Miron, C.E. / Pinus, S. / Labarre, A. ...Sharon, I. / Stille, J. / Tjutrins, J. / Wang, G. / Venegas, F.A. / Hennecker, C. / Rueda, A.M. / Miron, C.E. / Pinus, S. / Labarre, A. / Patrascu, M.B. / Vlaho, D. / Huot, M. / Mittermaier, A.K. / Moitessier, N. / Schmeing, T.M. | ||||||
![]() | ![]() Title: Design, synthesis and in vitro evaluation of novel SARS-CoV-2 3CL pro covalent inhibitors. Authors: Stille, J.K. / Tjutrins, J. / Wang, G. / Venegas, F.A. / Hennecker, C. / Rueda, A.M. / Sharon, I. / Blaine, N. / Miron, C.E. / Pinus, S. / Labarre, A. / Plescia, J. / Burai Patrascu, M. / ...Authors: Stille, J.K. / Tjutrins, J. / Wang, G. / Venegas, F.A. / Hennecker, C. / Rueda, A.M. / Sharon, I. / Blaine, N. / Miron, C.E. / Pinus, S. / Labarre, A. / Plescia, J. / Burai Patrascu, M. / Zhang, X. / Wahba, A.S. / Vlaho, D. / Huot, M.J. / Schmeing, T.M. / Mittermaier, A.K. / Moitessier, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.8 KB | Display | ![]() |
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PDB format | ![]() | 54 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 764.9 KB | Display | ![]() |
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Full document | ![]() | 765.6 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mlgC ![]() 6y2eS 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: 33550.246 Da / Num. of mol.: 1 / Fragment: UNP residues 3264-3567 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rep, 1a-1b / Production host: ![]() ![]() References: UniProt: P0DTD1, SARS coronavirus main proteinase |
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#2: Chemical | ChemComp-C7A / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.06 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 30% PEG2000 MME, 0.1 M potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.52131 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→38.4 Å / Num. obs: 8666 / % possible obs: 93.18 % / Redundancy: 1.9 % / CC1/2: 0.996 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.6→2.693 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 0.45 / Num. unique obs: 1645 / CC1/2: 0.679 / % possible all: 48.82 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 6Y2E Resolution: 2.6→38.4 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 23.329 / SU ML: 0.431 / Cross valid method: THROUGHOUT / ESU R Free: 0.404 / 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: 60.609 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→38.4 Å
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Refine LS restraints |
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