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Yorodumi- PDB-7mlg: Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) Coval... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mlg | ||||||
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Title | Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) Covalently Bound to Compound C63 | ||||||
Components | 3C-like proteinase | ||||||
Keywords | HYDROLASE/INHIBITOR / SARS-CoV-2 / 3CLpro / covalent inhibitor / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / symbiont-mediated suppression of host NF-kappaB cascade / 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 / 3'-5'-RNA exonuclease activity / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / 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 / 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 / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / 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 perinuclear region of cytoplasm / viral protein processing / host cell endoplasmic reticulum membrane / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / viral translational frameshifting / 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 | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mlg.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mlg.ent.gz | 54.4 KB | Display | PDB format |
PDBx/mmJSON format | 7mlg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mlg_validation.pdf.gz | 758.4 KB | Display | wwPDB validaton report |
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Full document | 7mlg_full_validation.pdf.gz | 760.6 KB | Display | |
Data in XML | 7mlg_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 7mlg_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/7mlg ftp://data.pdbj.org/pub/pdb/validation_reports/ml/7mlg | HTTPS FTP |
-Related structure data
Related structure data | 7mlfC 6y2eS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33825.547 Da / Num. of mol.: 1 / Fragment: UNP residues 3264-3569 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0DTD1, SARS coronavirus main proteinase |
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#2: Chemical | ChemComp-ZJ1 / ( |
#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: 2.01 Å3/Da / Density % sol: 38.68 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M BTP, pH 6.5, 20% PEG3350, 0.2 M potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.11 Å / Num. obs: 9329 / % possible obs: 97.9 % / Redundancy: 2.8 % / CC1/2: 0.998 / Net I/σ(I): 12.52 |
Reflection shell | Resolution: 2.5→2.59 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1710 / CC1/2: 0.786 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6Y2E Resolution: 2.5→48.11 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.906 / SU B: 21.642 / SU ML: 0.421 / Cross valid method: THROUGHOUT / ESU R Free: 0.37 / 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: 59.42 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→48.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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