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Yorodumi- PDB-7qck: Structure of SARS-CoV-2 Papain-like Protease bound to N-(2,5-dihy... -
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-Basic information
Entry | Database: PDB / ID: 7qck | |||||||||||||||
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Title | Structure of SARS-CoV-2 Papain-like Protease bound to N-(2,5-dihydroxybenzylidene)-thiosemicarbazone | |||||||||||||||
Components | Papain-like protease nsp3 | |||||||||||||||
Keywords | HYDROLASE / Cystein-Protease / Inhibitor / SARS-CoV-2 / Thiosemicarbazone / Deubiquitination | |||||||||||||||
Function / homology | Function and homology information viral genome replication / methyltransferase 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 / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase ...viral genome replication / methyltransferase 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 / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / 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 / methylation / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease 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 / host cell endoplasmic reticulum membrane / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / lipid binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding / membrane Similarity search - Function | |||||||||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | |||||||||||||||
Authors | Ewert, W. / Gunther, S. / Reinke, P. / Falke, S. / Lieske, J. / Miglioli, F. / Carcelli, M. / Srinivasan, V. / Betzel, C. / Han, H. ...Ewert, W. / Gunther, S. / Reinke, P. / Falke, S. / Lieske, J. / Miglioli, F. / Carcelli, M. / Srinivasan, V. / Betzel, C. / Han, H. / Lorenzen, K. / Guenther, C. / Niebling, S. / Garcia-Alai, M. / Hinrichs, W. / Rogolino, D. / Meents, A. | |||||||||||||||
Funding support | Germany, 4items
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Citation | Journal: Front Chem / Year: 2022 Title: Hydrazones and Thiosemicarbazones Targeting Protein-Protein-Interactions of SARS-CoV-2 Papain-like Protease. Authors: Ewert, W. / Gunther, S. / Miglioli, F. / Falke, S. / Reinke, P.Y.A. / Niebling, S. / Gunther, C. / Han, H. / Srinivasan, V. / Brognaro, H. / Lieske, J. / Lorenzen, K. / Garcia-Alai, M.M. / ...Authors: Ewert, W. / Gunther, S. / Miglioli, F. / Falke, S. / Reinke, P.Y.A. / Niebling, S. / Gunther, C. / Han, H. / Srinivasan, V. / Brognaro, H. / Lieske, J. / Lorenzen, K. / Garcia-Alai, M.M. / Betzel, C. / Carcelli, M. / Hinrichs, W. / Rogolino, D. / Meents, A. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qck.cif.gz | 147.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qck.ent.gz | 108.2 KB | Display | PDB format |
PDBx/mmJSON format | 7qck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qck_validation.pdf.gz | 736.4 KB | Display | wwPDB validaton report |
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Full document | 7qck_full_validation.pdf.gz | 739.7 KB | Display | |
Data in XML | 7qck_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 7qck_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/7qck ftp://data.pdbj.org/pub/pdb/validation_reports/qc/7qck | HTTPS FTP |
-Related structure data
Related structure data | 7qcgC 7qchC 7qciC 7qcjC 7qcmC 7nfvS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35687.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0DTC1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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-Non-polymers , 6 types, 204 molecules
#2: Chemical | ChemComp-A7L / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-ZN / | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | 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: 3.77 Å3/Da / Density % sol: 67.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris-HCl pH 8.0, 10% glycerol, 0.8 M sodium dihydrogenphosphate, 1.2 M potassium hydrogenphosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→49.16 Å / Num. obs: 41889 / % possible obs: 99.88 % / Redundancy: 10.6 % / Biso Wilson estimate: 39.12 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.33 |
Reflection shell | Resolution: 1.92→1.989 Å / Num. unique obs: 4128 / CC1/2: 0.624 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7nfv Resolution: 1.92→49.16 Å / SU ML: 0.2866 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.2051 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: 49.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→49.16 Å
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Refine LS restraints |
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LS refinement shell |
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