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Yorodumi- PDB-7rnw: SARS-CoV-2 Main Protease in complex with a cyclic peptide inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rnw | ||||||
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Title | SARS-CoV-2 Main Protease in complex with a cyclic peptide inhibitor | ||||||
Components |
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Keywords | Hydrolase/Hydrolase Inhibitor / Protease / drug design / complex / COVID-19 / VIRAL PROTEIN / Hydrolase-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 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Frkic, R.L. / Jackson, C.J. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Chem Sci / Year: 2022 Title: Antiviral cyclic peptides targeting the main protease of SARS-CoV-2. Authors: Johansen-Leete, J. / Ullrich, S. / Fry, S.E. / Frkic, R. / Bedding, M.J. / Aggarwal, A. / Ashhurst, A.S. / Ekanayake, K.B. / Mahawaththa, M.C. / Sasi, V.M. / Luedtke, S. / Ford, D.J. / ...Authors: Johansen-Leete, J. / Ullrich, S. / Fry, S.E. / Frkic, R. / Bedding, M.J. / Aggarwal, A. / Ashhurst, A.S. / Ekanayake, K.B. / Mahawaththa, M.C. / Sasi, V.M. / Luedtke, S. / Ford, D.J. / O'Donoghue, A.J. / Passioura, T. / Larance, M. / Otting, G. / Turville, S. / Jackson, C.J. / Nitsche, C. / Payne, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rnw.cif.gz | 249.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rnw.ent.gz | 201.2 KB | Display | PDB format |
PDBx/mmJSON format | 7rnw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/7rnw ftp://data.pdbj.org/pub/pdb/validation_reports/rn/7rnw | HTTPS FTP |
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-Related structure data
Related structure data | 7jkvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33825.547 Da / Num. of mol.: 4 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 #2: Protein/peptide | Mass: 1912.128 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 3350, 0.1M Bis-Tris pH 6.0, 0.3M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2021 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.35→33.62 Å / Num. obs: 44063 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.989 / Rmerge(I) obs: 0.254 / Rpim(I) all: 0.103 / Rrim(I) all: 0.275 / Net I/σ(I): 6.4 / Num. measured all: 307728 / Scaling rejects: 3 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 6.9 %
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JKV Resolution: 2.35→33.62 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.912 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 112.44 Å2 / Biso mean: 34.931 Å2 / Biso min: 12.65 Å2
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Refinement step | Cycle: final / Resolution: 2.35→33.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.409 Å / Rfactor Rfree error: 0
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