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Yorodumi- PDB-7llf: SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-83 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7llf | ||||||
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Title | SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-83 | ||||||
Components | Non-structural protein 3 | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / papain-like protease / coronavirus inhibitor / SARS-CoV-2 / VIRAL PROTEIN / VIRAL PROTEIN-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 / methylation / 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 / Replication of the SARS-CoV-2 genome / methylation / 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: 2.3 Å | ||||||
Authors | Ratia, K.M. / Xiong, R. / Thatcher, G.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biorxiv / Year: 2021 Title: Potent, Novel SARS-CoV-2 PLpro Inhibitors Block Viral Replication in Monkey and Human Cell Cultures. Authors: Shen, Z. / Ratia, K. / Cooper, L. / Kong, D. / Lee, H. / Kwon, Y. / Li, Y. / Alqarni, S. / Huang, F. / Dubrovskyi, O. / Rong, L. / Thatcher, G.R. / Xiong, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7llf.cif.gz | 141.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7llf.ent.gz | 109.2 KB | Display | PDB format |
PDBx/mmJSON format | 7llf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/7llf ftp://data.pdbj.org/pub/pdb/validation_reports/ll/7llf | HTTPS FTP |
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-Related structure data
Related structure data | 7lbrC 7lbsC 7llzC 7losC 7jrnS C: citing same article (ref.) 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35758.578 Da / Num. of mol.: 2 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 , 6 types, 46 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-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: 2.81 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MIB buffer pH 6.5, 0.2M (NH4)2SO4, 13-16% PEG 3350, 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→46.29 Å / Num. obs: 33851 / % possible obs: 95.1 % / Redundancy: 3.3 % / CC1/2: 0.988 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.106 / Rrim(I) all: 0.196 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2626 / CC1/2: 0.148 / % possible all: 76.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JRN Resolution: 2.3→46.29 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 13.227 / SU ML: 0.272 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.348 / ESU R Free: 0.248 / 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: 167.53 Å2 / Biso mean: 52.873 Å2 / Biso min: 27.95 Å2
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Refinement step | Cycle: final / Resolution: 2.3→46.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0
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