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Yorodumi- PDB-8uvm: SARS-CoV-2 papain-like protease (PLpro) complex with covalent inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8uvm | ||||||
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Title | SARS-CoV-2 papain-like protease (PLpro) complex with covalent inhibitor Jun11313 | ||||||
Components | Papain-like protease nsp3 | ||||||
Keywords | VIRAL PROTEIN / HYDROLASE/INHIBITOR / SARS CoV-2 Papain Like protease complex / Covalent inhibitor / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 ...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 / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 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 / 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 / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / 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 | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Ansari, A. / Tan, B. / Chopra, A. / Ruiz, 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 | 8uvm.cif.gz | 322.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8uvm.ent.gz | 211.2 KB | Display | PDB format |
PDBx/mmJSON format | 8uvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8uvm_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8uvm_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8uvm_validation.xml.gz | 49.7 KB | Display | |
Data in CIF | 8uvm_validation.cif.gz | 65.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/8uvm ftp://data.pdbj.org/pub/pdb/validation_reports/uv/8uvm | HTTPS FTP |
-Related structure data
Related structure data | 8uobC 8uufC 8uugC 8uuhC 8uuuC 8uuvC 8uuwC 8uuyC 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 35943.762 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli) References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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-Non-polymers , 5 types, 202 molecules
#2: Chemical | ChemComp-Y3R / Mass: 521.628 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H31N3O5S / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-ZN / #6: 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: 4.13 Å3/Da / Density % sol: 70.25 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 2.5M Ammonium Sulfate, 0.1M Sodium citrate dibasic trihydrate pH 6.7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 29, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→42 Å / Num. obs: 55567 / % possible obs: 99.8 % / Redundancy: 18.9 % / Biso Wilson estimate: 59.44 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.043 / Rrim(I) all: 0.193 / Net I/σ(I): 10.67 |
Reflection shell | Resolution: 2.85→2.9 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.944 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2673 / CC1/2: 0.472 / Rpim(I) all: 0.309 / Rrim(I) all: 0.998 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→41.9 Å / Cross valid method: FREE R-VALUE / σ(F): 736.04 / Phase error: 27.0223 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: 65.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→41.9 Å
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Refine LS restraints |
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LS refinement shell |
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