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Yorodumi- PDB-7k6e: SARS-CoV-2 Main Protease Co-Crystal Structure with Telaprevir Det... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7k6e | |||||||||||||||
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Title | SARS-CoV-2 Main Protease Co-Crystal Structure with Telaprevir Determined from Crystals Grown with 40 nL Acoustically Ejected Mpro Droplets at 1.63 A Resolution (Direct Vitrification) | |||||||||||||||
Components | 3C-like proteinase | |||||||||||||||
Keywords | VIRAL PROTEIN / HYDROLASE/INHIBITOR / SARS-CoV-2 / Main Protease / 3CLpro/Mpro / Telaprevir / Acoustic Drop Ejection / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / snRNP Assembly / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / : / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / 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 / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / copper ion binding / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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: 1.63 Å | |||||||||||||||
Authors | Kreitler, D.F. / Andi, B. / Kumaran, D. / Soares, A.S. / Shi, W. / Jakoncic, J. / Fuchs, M.R. / Keereetaweep, J. / Shanklin, J. / McSweeney, S. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Sci Rep / Year: 2022 Title: Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease. Authors: Andi, B. / Kumaran, D. / Kreitler, D.F. / Soares, A.S. / Keereetaweep, J. / Jakoncic, J. / Lazo, E.O. / Shi, W. / Fuchs, M.R. / Sweet, R.M. / Shanklin, J. / Adams, P.D. / Schmidt, J.G. / ...Authors: Andi, B. / Kumaran, D. / Kreitler, D.F. / Soares, A.S. / Keereetaweep, J. / Jakoncic, J. / Lazo, E.O. / Shi, W. / Fuchs, M.R. / Sweet, R.M. / Shanklin, J. / Adams, P.D. / Schmidt, J.G. / Head, M.S. / McSweeney, S. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7k6e.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7k6e.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 7k6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/7k6e ftp://data.pdbj.org/pub/pdb/validation_reports/k6/7k6e | HTTPS FTP |
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-Related structure data
Related structure data | 7jycSC 7k3tC 7k40C 7k6dC 7mngC 7mrrC 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 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 (E. coli) References: UniProt: P0DTD1, SARS coronavirus main proteinase |
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#2: Chemical | ChemComp-DMS / |
#3: Chemical | ChemComp-SV6 / ( |
#4: 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: 2.1 Å3/Da / Density % sol: 41.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 22% PEG 4000, 100 mM HEPES pH 7.0, 3% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→53.75 Å / Num. obs: 34940 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 28.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.044 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.63→1.66 Å / Redundancy: 10.3 % / Rmerge(I) obs: 3.347 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1827 / CC1/2: 0.368 / Rpim(I) all: 1.091 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JYC Resolution: 1.63→53.75 Å / SU ML: 0.2352 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9595 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 36.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→53.75 Å
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Refine LS restraints |
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LS refinement shell |
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