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Yorodumi- PDB-8uho: Crystal structure of SARS CoV-2 3CL protease in complex with GSK4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8uho | ||||||
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Title | Crystal structure of SARS CoV-2 3CL protease in complex with GSK4365096A | ||||||
Components | 3C-like proteinase nsp5 | ||||||
Keywords | HYDROLASE / 3CL protease / SARS / viral protein | ||||||
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 / 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 / methylation / 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 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: 2.02 Å | ||||||
Authors | Concha, N.O. / Williams, S.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Bioorg.Med.Chem. / Year: 2024 Title: Exploration of the P1 residue in 3CL protease inhibitors leading to the discovery of a 2-tetrahydrofuran P1 replacement. Authors: Barton, L.S. / Callahan, J.F. / Cantizani, J. / Concha, N.O. / Cotillo Torrejon, I. / Goodwin, N.C. / Joshi-Pangu, A. / Kiesow, T.J. / McAtee, J.J. / Mellinger, M. / Nixon, C.J. / Padron- ...Authors: Barton, L.S. / Callahan, J.F. / Cantizani, J. / Concha, N.O. / Cotillo Torrejon, I. / Goodwin, N.C. / Joshi-Pangu, A. / Kiesow, T.J. / McAtee, J.J. / Mellinger, M. / Nixon, C.J. / Padron-Barthe, L. / Patterson, J.R. / Pearson, N.D. / Pouliot, J.J. / Rendina, A.R. / Buitrago Santanilla, A. / Schneck, J.L. / Sanz, O. / Thalji, R.K. / Ward, P. / Williams, S.P. / King, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8uho.cif.gz | 421 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8uho.ent.gz | 290.1 KB | Display | PDB format |
PDBx/mmJSON format | 8uho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8uho_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8uho_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8uho_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 8uho_validation.cif.gz | 36.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/8uho ftp://data.pdbj.org/pub/pdb/validation_reports/uh/8uho | HTTPS FTP |
-Related structure data
Related structure data | 8uiaC 8uifC 8uldC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
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-Components
#1: Protein | Mass: 33825.547 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, SARS coronavirus main proteinase #2: Chemical | Mass: 623.712 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H42FN3O7 / Feature type: SUBJECT OF INVESTIGATION #3: Water | ChemComp-HOH / | 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: 2.59 Å3/Da / Density % sol: 52.53 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 4.6 Details: 0.02M CaCl2, 30% MPD, 01 M sodium acetate, pH 4.6 Crystals grew over night with seeding and were left to grow for up to two days before they were harvested |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→50 Å / Num. obs: 46504 / % possible obs: 99.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 24.65 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.068 / Net I/σ(I): 27.9 |
Reflection shell | Resolution: 2.02→2.05 Å / Rmerge(I) obs: 0.45 / Num. unique obs: 2266 / CC1/2: 0.921 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→41.02 Å / SU ML: 0.1775 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2628 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: 31.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→41.02 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.828299055835 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -2.19848794207 Å / Origin y: -2.79880488156 Å / Origin z: 16.1252760746 Å
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Refinement TLS group | Selection details: all |