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Yorodumi- PDB-7m03: Structure of SARS-CoV-2 3CL protease in complex with inhibitor 18c -
+Open data
-Basic information
Entry | Database: PDB / ID: 7m03 | ||||||
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Title | Structure of SARS-CoV-2 3CL protease in complex with inhibitor 18c | ||||||
Components | 3C-like proteinase | ||||||
Keywords | HYDROLASE/INHIBITOR / COVID-19 / PROTEASE / severe acute respiratory syndrome coronavirus 2 / SARS-CoV-2 3CL protease Inhhibitors / 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 / symbiont-mediated suppression of host NF-kappaB cascade / 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 / 3'-5'-RNA exonuclease activity / SARS coronavirus main proteinase / 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 / 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 / viral protein processing / host cell endoplasmic reticulum membrane / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / viral translational frameshifting / 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 Å | ||||||
Authors | Kashipathy, M.M. / Lovell, S. / Battaile, K.P. / Chamandi, S.D. / Rathnayake, A.D. / Kim, Y. / Perera, K.D. / Jesri, A.R.M. / Nguyen, H.N. / Baird, M.A. ...Kashipathy, M.M. / Lovell, S. / Battaile, K.P. / Chamandi, S.D. / Rathnayake, A.D. / Kim, Y. / Perera, K.D. / Jesri, A.R.M. / Nguyen, H.N. / Baird, M.A. / Miller, M.J. / Groutas, W.C. / Chang, K.O. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2021 Title: Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies. Authors: Dampalla, C.S. / Rathnayake, A.D. / Perera, K.D. / Jesri, A.M. / Nguyen, H.N. / Miller, M.J. / Thurman, H.A. / Zheng, J. / Kashipathy, M.M. / Battaile, K.P. / Lovell, S. / Perlman, S. / Kim, ...Authors: Dampalla, C.S. / Rathnayake, A.D. / Perera, K.D. / Jesri, A.M. / Nguyen, H.N. / Miller, M.J. / Thurman, H.A. / Zheng, J. / Kashipathy, M.M. / Battaile, K.P. / Lovell, S. / Perlman, S. / Kim, Y. / Groutas, W.C. / Chang, K.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7m03.cif.gz | 131.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m03.ent.gz | 99.2 KB | Display | PDB format |
PDBx/mmJSON format | 7m03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7m03_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7m03_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7m03_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 7m03_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/7m03 ftp://data.pdbj.org/pub/pdb/validation_reports/m0/7m03 | HTTPS FTP |
-Related structure data
Related structure data | 7lztC 7lzuC 7lzvC 7lzwC 7lzxC 7lzyC 7lzzC 7m00C 7m01C 7m02C 7m04C 6xmkS 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
#1: Protein | Mass: 34068.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: P0DTD1, SARS coronavirus main proteinase #2: Chemical | #3: Chemical | #4: 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: 2.22 Å3/Da / Density % sol: 44.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% w/v PEG2000 MME, 100 mM potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2020 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2→49.31 Å / Num. obs: 39124 / % possible obs: 97.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 35.93 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Net I/σ(I): 10.3 / Num. measured all: 136296 / Scaling rejects: 1 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.5 %
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6XMK Resolution: 2→36.91 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.11 / Phase error: 29.43 / 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: 109.04 Å2 / Biso mean: 45.622 Å2 / Biso min: 22.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→36.91 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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