+Open data
-Basic information
Entry | Database: PDB / ID: 8uuf | ||||||
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Title | SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun11941 | ||||||
Components | Papain-like protease nsp3 | ||||||
Keywords | VIRAL PROTEIN / HYDROLASE/INHIBITOR / SARS-CoV-2 Papain-Like protease / HYDROLASE-INHIBITOR complex | ||||||
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 / methylation / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane ...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 / methylation / 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 / 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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / symbiont-mediated suppression of host gene expression / cysteine-type endopeptidase activity / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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: 2.84 Å | ||||||
Authors | Ansari, A. / Tan, B. / Riuz, F.X. / Arnold, E. / Wang, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2024 Title: Design of a SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model. Authors: Tan, B. / Zhang, X. / Ansari, A. / Jadhav, P. / Tan, H. / Li, K. / Chopra, A. / Ford, A. / Chi, X. / Ruiz, F.X. / Arnold, E. / Deng, X. / Wang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8uuf.cif.gz | 86.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8uuf.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 8uuf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/8uuf ftp://data.pdbj.org/pub/pdb/validation_reports/uu/8uuf | HTTPS FTP |
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-Related structure data
Related structure data | 8uobC 8uugC 8uuhC 8uuuC 8uuvC 8uuwC 8uuyC 8uvmC 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35943.762 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 (E. coli) / References: UniProt: P0DTC1, ubiquitinyl hydrolase 1 |
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-Non-polymers , 5 types, 110 molecules
#2: Chemical | ChemComp-XWO / Mass: 486.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H34N6O2 / Feature type: SUBJECT OF INVESTIGATION | ||||
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#3: Chemical | ChemComp-ACT / | ||||
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-CL / #6: 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: 5 Å3/Da / Density % sol: 75.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4 / Details: 0.2M Zinc acetate, 0.1M Bis Tris, 10% PEG 8000 / PH range: 5.5-6.5 |
-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-2 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 23, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→29.08 Å / Num. obs: 17605 / % possible obs: 99.7 % / Redundancy: 13.3 % / Biso Wilson estimate: 63.03 Å2 / CC1/2: 0.99 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.84→2.99 Å / Num. unique obs: 2480 / CC1/2: 0.905 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→29.08 Å / SU ML: 0.3479 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1122 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.84→29.08 Å
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Refine LS restraints |
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LS refinement shell |
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