[English] 日本語
Yorodumi- PDB-8uuy: SARS-CoV-2 papain-like protease (PLpro) complex with inhibitor Ju... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8uuy | ||||||
---|---|---|---|---|---|---|---|
Title | SARS-CoV-2 papain-like protease (PLpro) complex with inhibitor Jun12129 | ||||||
Components | Papain-like protease nsp3 | ||||||
Keywords | VIRAL PROTEIN / HYDROLASE/INHIBITOR / SARS-CoV-2 papain-like protease (PLpro) / complex / Inhibitor / 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 / 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: 3.05 Å | ||||||
Authors | Ansari, A. / Tan, B. / Ruiz, F.X. / Arnold, E. / Wang, J. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8uuy.cif.gz | 89.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8uuy.ent.gz | 60.7 KB | Display | PDB format |
PDBx/mmJSON format | 8uuy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8uuy_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8uuy_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8uuy_validation.xml.gz | 15 KB | Display | |
Data in CIF | 8uuy_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/8uuy ftp://data.pdbj.org/pub/pdb/validation_reports/uu/8uuy | HTTPS FTP |
-Related structure data
Related structure data | 8uobC 8uufC 8uugC 8uuhC 8uuuC 8uuvC 8uuwC 8uvmC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-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 |
---|
-Non-polymers , 7 types, 115 molecules
#2: Chemical | ChemComp-Y2R / Mass: 519.721 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H33N3O2S2 / Feature type: SUBJECT OF INVESTIGATION | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-PEG / | ||||
#4: Chemical | ChemComp-PGE / | ||||
#5: Chemical | ChemComp-ACT / | ||||
#6: Chemical | ChemComp-ZN / #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.96 Å3/Da / Density % sol: 75.2 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.2M Zinc Acetate, 0.1M BisTris pH 6.2, 8% PEG 8000 PH range: 5.5-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 26, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→100.92 Å / Num. obs: 14155 / % possible obs: 100 % / Redundancy: 26.4 % / Biso Wilson estimate: 86.1 Å2 / CC1/2: 0.997 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 3.05→3.26 Å / Num. unique obs: 2508 / CC1/2: 0.677 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→61.65 Å / SU ML: 0.421 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0116 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05→61.65 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|