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- PDB-7rvz: Structure of the SARS-CoV-2 main protease in complex with inhibit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rvz | ||||||
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Title | Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI26 | ||||||
![]() | 3C-like proteinase | ||||||
![]() | VIRAL PROTEIN / HYDROLASE/INHIBITOR / COVID-19 / SARS-CoV-2 / main protease / reversible covalent inhibitors / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() 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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, K. / Sankaran, B. / Liu, W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals. Authors: Ma, Y. / Yang, K.S. / Geng, Z.Z. / Alugubelli, Y.R. / Shaabani, N. / Vatansever, E.C. / Ma, X.R. / Cho, C.C. / Khatua, K. / Xiao, J. / Blankenship, L.R. / Yu, G. / Sankaran, B. / Li, P. / ...Authors: Ma, Y. / Yang, K.S. / Geng, Z.Z. / Alugubelli, Y.R. / Shaabani, N. / Vatansever, E.C. / Ma, X.R. / Cho, C.C. / Khatua, K. / Xiao, J. / Blankenship, L.R. / Yu, G. / Sankaran, B. / Li, P. / Allen, R. / Ji, H. / Xu, S. / Liu, W.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.5 KB | Display | ![]() |
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PDB format | ![]() | 106.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 774.2 KB | Display | ![]() |
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Full document | ![]() | 777.8 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rvmC ![]() 7rvnC ![]() 7rvoC ![]() 7rvpC ![]() 7rvqC ![]() 7rvrC ![]() 7rvsC ![]() 7rvtC ![]() 7rvuC ![]() 7rvvC ![]() 7rvwC ![]() 7rvxC ![]() 7rvyC ![]() 7rw0C ![]() 7rw1C ![]() 7jpyS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 33767.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rep, 1a-1b / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-7YW / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.49 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.2 M Ammonium phosphate dibasic, 17% w/v PEG3350, pH8.0 |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99988 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→59.88 Å / Num. obs: 27791 / % possible obs: 96.1 % / Redundancy: 6.4 % / CC1/2: 0.997 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.9→1.94 Å / Num. unique obs: 1767 / CC1/2: 0.674 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7JPY Resolution: 1.9→43.45 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.23 / 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: 127.17 Å2 / Biso mean: 44.8371 Å2 / Biso min: 21.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→43.45 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: -13.1424 Å / Origin y: -14.706 Å / Origin z: -0.5476 Å
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Refinement TLS group |
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