+Open data
-Basic information
Entry | Database: PDB / ID: 7nwx | ||||||
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Title | SARS-COV2 NSP5 in the presence of Zn2+ | ||||||
Components | Replicase polyprotein 1a | ||||||
Keywords | VIRAL PROTEIN / SARS-CoV2 / NSP5 / 3C-like proteinase / coronavirus | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Calderone, V. / Grifagni, D. / Cantini, F. / Fragai, M. / Banci, L. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2021 Title: SARS-CoV-2 M pro inhibition by a zinc ion: structural features and hints for drug design. Authors: Grifagni, D. / Calderone, V. / Giuntini, S. / Cantini, F. / Fragai, M. / Banci, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nwx.cif.gz | 132.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nwx.ent.gz | 102.7 KB | Display | PDB format |
PDBx/mmJSON format | 7nwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/7nwx ftp://data.pdbj.org/pub/pdb/validation_reports/nw/7nwx | HTTPS FTP |
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-Related structure data
Related structure data | 7nxhC 6yb7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33825.547 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 |
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#2: Chemical | ChemComp-ZN / |
#3: 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: 1.97 Å3/Da / Density % sol: 37.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium acetate, 20% PEG 3350, 1.5 mM zinc chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.541 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Feb 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48.18 Å / Num. obs: 40960 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.8→1.91 Å / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1891 / CC1/2: 0.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6yb7 Resolution: 1.8→31.42 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 28.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.72 Å2 / Biso mean: 24.6996 Å2 / Biso min: 11.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→31.42 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: -16.9096 Å / Origin y: -26.0833 Å / Origin z: 17.0748 Å
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Refinement TLS group |
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