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Yorodumi- PDB-7sgw: Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder630 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sgw | ||||||
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Title | Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder630 inhibitor | ||||||
Components | Non-structural protein 3 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / COVID-19 / coronavirus / SARS / COV-2 / papain-like protease / IDP51000 / IDP52003 / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / HYDROLASE-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 / 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 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / methylation / 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: 1.95 Å | ||||||
Authors | Osipiuk, J. / Tesar, C. / Endres, M. / Lisnyak, V. / Maki, S. / Taylor, C. / Zhang, Y. / Zhou, Z. / Azizi, S.A. / Jones, K. ...Osipiuk, J. / Tesar, C. / Endres, M. / Lisnyak, V. / Maki, S. / Taylor, C. / Zhang, Y. / Zhou, Z. / Azizi, S.A. / Jones, K. / Kathayat, R. / Snyder, S.A. / Dickinson, B.C. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder630 inhibitor Authors: Osipiuk, J. / Tesar, C. / Endres, M. / Lisnyak, V. / Maki, S. / Taylor, C. / Zhang, Y. / Zhou, Z. / Azizi, S.A. / Jones, K. / Kathayat, R. / Snyder, S.A. / Dickinson, B.C. / Joachimiak, A. / ...Authors: Osipiuk, J. / Tesar, C. / Endres, M. / Lisnyak, V. / Maki, S. / Taylor, C. / Zhang, Y. / Zhou, Z. / Azizi, S.A. / Jones, K. / Kathayat, R. / Snyder, S.A. / Dickinson, B.C. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sgw.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sgw.ent.gz | 112.4 KB | Display | PDB format |
PDBx/mmJSON format | 7sgw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/7sgw ftp://data.pdbj.org/pub/pdb/validation_reports/sg/7sgw | HTTPS FTP |
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-Related structure data
Related structure data | 6wrhS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35943.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Three N-terminal residues (SNA) are expression tag Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0DTC1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase |
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#2: Chemical | ChemComp-L30 / |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 66.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Bis_tris propane, pH 7.0, 2.5 M ammonium sulfate, 4 mM PLP_Snyder630 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Sep 16, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→49.05 Å / Num. obs: 39163 / % possible obs: 99.8 % / Redundancy: 9.3 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.041 / Rrim(I) all: 0.132 / Χ2: 1.57 / Net I/av σ(I): 20.8 / Net I/σ(I): 10 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WRH Resolution: 1.95→49.05 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.323 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 112.18 Å2 / Biso mean: 46.743 Å2 / Biso min: 32.58 Å2
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Refinement step | Cycle: final / Resolution: 1.95→49.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 4.604 Å / Origin y: 80.5508 Å / Origin z: 29.0256 Å
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