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Yorodumi- PDB-9eor: SARS-CoV2 major protease in complex with a covalent inhibitor SLL12. -
+Open data
-Basic information
Entry | Database: PDB / ID: 9eor | |||||||||
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Title | SARS-CoV2 major protease in complex with a covalent inhibitor SLL12. | |||||||||
Components |
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Keywords | ANTIVIRAL PROTEIN / 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 / 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 / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated suppression of host NF-kappaB cascade / 5'-3' DNA helicase activity / 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 / mRNA (guanine-N7)-methyltransferase / omega peptidase activity / methyltransferase cap1 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / 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 / host cell perinuclear region of cytoplasm / single-stranded RNA binding / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral translational frameshifting / RNA-directed RNA polymerase / copper ion binding / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / lipid binding / DNA-templated transcription / 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: 2.25 Å | |||||||||
Authors | Moche, M. / Lennerstrand, J. / Nyman, T. / Strandback, E. / Akaberi, D. | |||||||||
Funding support | Sweden, 1items
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Citation | Journal: Antimicrob.Agents Chemother. / Year: 2024 Title: Identification of novel and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries. Authors: Akaberi, D. / Pourghasemi Lati, M. / Krambrich, J. / Berger, J. / Neilsen, G. / Strandback, E. / Turunen, S.P. / Wannberg, J. / Gullberg, H. / Moche, M. / Chinthakindi, P.K. / Nyman, T. / ...Authors: Akaberi, D. / Pourghasemi Lati, M. / Krambrich, J. / Berger, J. / Neilsen, G. / Strandback, E. / Turunen, S.P. / Wannberg, J. / Gullberg, H. / Moche, M. / Chinthakindi, P.K. / Nyman, T. / Sarafianos, S.G. / Sandstrom, A. / Jarhult, J.D. / Sandberg, K. / Lundkvist, A. / Verho, O. / Lennerstrand, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9eor.cif.gz | 371.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9eor.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9eor.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9eor_validation.pdf.gz | 507.5 KB | Display | wwPDB validaton report |
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Full document | 9eor_full_validation.pdf.gz | 546.8 KB | Display | |
Data in XML | 9eor_validation.xml.gz | 78.9 KB | Display | |
Data in CIF | 9eor_validation.cif.gz | 102.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/9eor ftp://data.pdbj.org/pub/pdb/validation_reports/eo/9eor | HTTPS FTP |
-Related structure data
Related structure data | 9eo6C 9eoxC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 33825.547 Da / Num. of mol.: 6 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: 624.733 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-K / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
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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: 2.68 Å3/Da / Density % sol: 54.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% w/v PEG3350 0.2M potassium-thiocyanate 0.1M bis-tris propane pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976254 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→43.91 Å / Num. obs: 58705 / % possible obs: 58.8 % / Redundancy: 3.5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.098 / Rrim(I) all: 0.186 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.25→2.44 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2937 / CC1/2: 0.597 / Rpim(I) all: 0.433 / Rrim(I) all: 0.812 / % possible all: 13.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→43.91 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.847 / SU B: 11.284 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R Free: 0.407 / 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: 33.558 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→43.91 Å
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