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- PDB-7l8i: SARS-CoV-2 Main Protease (Mpro) in Complex with Rupintrivir (P21) -
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Open data
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Basic information
Entry | Database: PDB / ID: 7l8i | |||||||||
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Title | SARS-CoV-2 Main Protease (Mpro) in Complex with Rupintrivir (P21) | |||||||||
![]() | 3C-like proteinase | |||||||||
![]() | HYDROLASE/INHIBITOR / SARS-CoV-2 / SARS2 / COVID19 / PROTEASE / PROTEASE INHIBITOR / COMPLEX / HYDROLASE INHIBITOR COMPLEX / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / RUPINTRIVIR / 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 | ![]() ![]() | |||||||||
![]() | Lockbaum, G.J. / Henes, M. / Lee, J.M. / Timm, J. / Nalivaika, E.A. / Yilmaz, N.K. / Thompson, P.R. / Schiffer, C.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Pan-3C Protease Inhibitor Rupintrivir Binds SARS-CoV-2 Main Protease in a Unique Binding Mode. Authors: Lockbaum, G.J. / Henes, M. / Lee, J.M. / Timm, J. / Nalivaika, E.A. / Thompson, P.R. / Kurt Yilmaz, N. / Schiffer, C.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 230.8 KB | Display | ![]() |
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PDB format | ![]() | 185.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 956.8 KB | Display | ![]() |
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Full document | ![]() | 966.2 KB | Display | |
Data in XML | ![]() | 27.5 KB | Display | |
Data in CIF | ![]() | 38.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7l8hC ![]() 7l8jC ![]() 6m03S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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
#1: Protein | Mass: 33825.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rep, 1a-1b / Production host: ![]() ![]() References: UniProt: P0DTD1, SARS coronavirus main proteinase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 22% (w/v) PEG 3350, 0.1 M Bis-Tris-Methane pH 5.5 and 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→23.74 Å / Num. obs: 28161 / % possible obs: 92.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 29.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08649 / Rpim(I) all: 0.05453 / Net I/σ(I): 9.05 |
Reflection shell | Resolution: 2.104→2.18 Å / Rmerge(I) obs: 0.3854 / Mean I/σ(I) obs: 3.09 / Num. unique obs: 2360 / CC1/2: 0.94 / Rpim(I) all: 0.248 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6M03 Resolution: 2.1→23.74 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.16 / 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: 136.02 Å2 / Biso mean: 39.3953 Å2 / Biso min: 12.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→23.74 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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