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- PDB-7los: SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-65 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7los | ||||||
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Title | SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-65 | ||||||
![]() | Non-structural protein 3 | ||||||
![]() | VIRAL PROTEIN/INHIBITOR / papain-like protease / coronavirus inhibitor / SARS-CoV-2 / VIRAL PROTEIN / VIRAL PROTEIN-INHIBITOR complex | ||||||
Function / homology | ![]() viral genome replication / methyltransferase activity / 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 ...viral genome replication / methyltransferase activity / 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 / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / endonuclease activity / methylation / 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 / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / lipid binding / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ratia, K.M. / Xiong, R. / Thatcher, G.R. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.5 KB | Display | ![]() |
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PDB format | ![]() | 108.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7lbrC ![]() 7lbsC ![]() 7llfC ![]() 7llzC ![]() 7jrnS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P0DTC1, UniProt: P0DTD1*PLUS, ubiquitinyl hydrolase 1 |
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-Non-polymers , 5 types, 27 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/Y97.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/Y97.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MIB buffer pH 6.5, 0.2 M (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: ![]() ![]() ![]() |
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: 2.9→48.73 Å / Num. obs: 17292 / % possible obs: 98.1 % / Redundancy: 3 % / CC1/2: 0.956 / Rpim(I) all: 0.164 / Rrim(I) all: 0.293 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2801 / CC1/2: 0.465 / Rpim(I) all: 0.654 / % possible all: 99.4 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 7JRN Resolution: 2.9→43.85 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.863 / SU B: 24.314 / SU ML: 0.422 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.488 / 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: 150.48 Å2 / Biso mean: 50.484 Å2 / Biso min: 17.1 Å2
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Refinement step | Cycle: final / Resolution: 2.9→43.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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