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- PDB-7ax6: Structure of SARS-CoV-2 Main Protease bound to Glutathione isopro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ax6 | |||||||||
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Title | Structure of SARS-CoV-2 Main Protease bound to Glutathione isopropyl ester | |||||||||
![]() | 3C-like proteinase | |||||||||
![]() | PEPTIDE BINDING PROTEIN / inhibitor / complex / screen / sars-cov-2 | |||||||||
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 / 3'-5'-RNA exonuclease activity / 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 / host cell endoplasmic reticulum membrane / 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 | ![]() ![]() ![]() | |||||||||
![]() | Guenther, S. / Reinke, P.Y.A. / Oberthuer, D. / Yefanov, O. / Gelisio, L. / Ginn, H. / Lieske, J. / Domaracky, M. / Brehm, W. / Rahmani Mashour, A. ...Guenther, S. / Reinke, P.Y.A. / Oberthuer, D. / Yefanov, O. / Gelisio, L. / Ginn, H. / Lieske, J. / Domaracky, M. / Brehm, W. / Rahmani Mashour, A. / White, T.A. / Knoska, J. / Pena Esperanza, G. / Koua, F. / Tolstikova, A. / Groessler, M. / Fischer, P. / Hennicke, V. / Fleckenstein, H. / Trost, F. / Galchenkova, M. / Gevorkov, Y. / Li, C. / Awel, S. / Paulraj, L.X. / Ullah, N. / Falke, S. / Alves Franca, B. / Schwinzer, M. / Brognaro, H. / Werner, N. / Perbandt, M. / Tidow, H. / Seychell, B. / Beck, T. / Meier, S. / Doyle, J.J. / Giseler, H. / Melo, D. / Lane, T.J. / Dunkel, I. / Peck, A. / Saouane, S. / Hakanpaeae, J. / Meyer, J. / Noei, H. / Gribbon, P. / Ellinger, B. / Kuzikov, M. / Wolf, M. / Zhang, L. / Ehrt, C. / Pletzer-Zelgert, J. / Wollenhaupt, J. / Feiler, C. / Weiss, M. / Schulz, E.C. / Mehrabi, P. / Norton-Baker, B. / Schmidt, C. / Lorenzen, K. / Schubert, R. / Han, H. / Chari, A. / Fernandez Garcia, Y. / Turk, D. / Hilgenfeld, R. / Rarey, M. / Zaliani, A. / Chapman, H.N. / Pearson, A. / Betzel, C. / Meents, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Authors: Gunther, S. / Reinke, P.Y.A. / Fernandez-Garcia, Y. / Lieske, J. / Lane, T.J. / Ginn, H.M. / Koua, F.H.M. / Ehrt, C. / Ewert, W. / Oberthuer, D. / Yefanov, O. / Meier, S. / Lorenzen, K. / ...Authors: Gunther, S. / Reinke, P.Y.A. / Fernandez-Garcia, Y. / Lieske, J. / Lane, T.J. / Ginn, H.M. / Koua, F.H.M. / Ehrt, C. / Ewert, W. / Oberthuer, D. / Yefanov, O. / Meier, S. / Lorenzen, K. / Krichel, B. / Kopicki, J.D. / Gelisio, L. / Brehm, W. / Dunkel, I. / Seychell, B. / Gieseler, H. / Norton-Baker, B. / Escudero-Perez, B. / Domaracky, M. / Saouane, S. / Tolstikova, A. / White, T.A. / Hanle, A. / Groessler, M. / Fleckenstein, H. / Trost, F. / Galchenkova, M. / Gevorkov, Y. / Li, C. / Awel, S. / Peck, A. / Barthelmess, M. / Schlunzen, F. / Lourdu Xavier, P. / Werner, N. / Andaleeb, H. / Ullah, N. / Falke, S. / Srinivasan, V. / Franca, B.A. / Schwinzer, M. / Brognaro, H. / Rogers, C. / Melo, D. / Zaitseva-Doyle, J.J. / Knoska, J. / Pena-Murillo, G.E. / Mashhour, A.R. / Hennicke, V. / Fischer, P. / Hakanpaa, J. / Meyer, J. / Gribbon, P. / Ellinger, B. / Kuzikov, M. / Wolf, M. / Beccari, A.R. / Bourenkov, G. / von Stetten, D. / Pompidor, G. / Bento, I. / Panneerselvam, S. / Karpics, I. / Schneider, T.R. / Garcia-Alai, M.M. / Niebling, S. / Gunther, C. / Schmidt, C. / Schubert, R. / Han, H. / Boger, J. / Monteiro, D.C.F. / Zhang, L. / Sun, X. / Pletzer-Zelgert, J. / Wollenhaupt, J. / Feiler, C.G. / Weiss, M.S. / Schulz, E.C. / Mehrabi, P. / Karnicar, K. / Usenik, A. / Loboda, J. / Tidow, H. / Chari, A. / Hilgenfeld, R. / Uetrecht, C. / Cox, R. / Zaliani, A. / Beck, T. / Rarey, M. / Gunther, S. / Turk, D. / Hinrichs, W. / Chapman, H.N. / Pearson, A.R. / Betzel, C. / Meents, A. #1: ![]() Title: Inhibition of SARS-CoV-2 main protease by allosteric drug-binding Authors: Guenther, S. / Reinke, P.Y.A., / Fernandez-Garcia, Y., / Lieske, J., / Lane, T.J., / Ginn, H.M., / Koua, F.H.M., / Ehrt, C., / Ewert, W., / Oberthuer, D., / Yefanov, O., / Meier, S., / ...Authors: Guenther, S. / Reinke, P.Y.A., / Fernandez-Garcia, Y., / Lieske, J., / Lane, T.J., / Ginn, H.M., / Koua, F.H.M., / Ehrt, C., / Ewert, W., / Oberthuer, D., / Yefanov, O., / Meier, S., / Lorenzen, K., / Krichel, B., / Kopicki, J.D., / Gelisio, L., / Brehm, W., / Dunkel , I., / Seychell , B., / Gieseler , H., / Norton-Baker , B., / Escudero-Perez, B., / Domaracky , M., / Saouane, S., / Tolstikova , A., / White, T.A., / Hanle, A., / Groessler , M., / Fleckenstein , H., / Trost , F., / Galchenkova , M., / Gevorkov , Y., / Li , C., / Awel , S., / Peck, A. / Barthelmess , M., / Schluenzen , F., / Paulraj , L.X., / Werner , N., / Andaleeb , H., / Ullah , N., / Falke , S., / Srinivasan, V., / Franca , B., / Schwinzer , M., / Brognaro , H., / Rogers , C., / Melo , D., / Doyle , J.J., / Knoska , J., / Pena Murillo, G.E., / Rahmani Mashhour, A., / Guicking , F., / Hennicke , V., / Fischer , P., / Hakanpaeae , J., / Meyer , J., / Gribbon , P., / Ellinger , B., / Kuzikov , M., / Wolf , M., / Burenkov, G., / von Stetten, D., / Pompidor, G., / Bento, I., / Panneerselvam, S., / Karpics, I., / Schneider , T.R., / Garcia Alai, M., / Niebling, S., / Guenther , C., / Schmidt , C., / Schubert , R., / Han , H., / Boger, J., / Monteiro , D., / Zhang, L., / Sun, X., / Pletzer-Zelgert , J., / Wollenhaupt , J., / Feiler , C., / Weiss , M., / Schulz , E.C., / Mehrabi , P., / Karnicar , K., / Usenik, A., / Loboda , J., / Tidow , H., / Chari , A., / Hilgenfeld , R., / Uetrecht , C., / Cox , R., / Zaliani , A., / Beck , T., / Rarey , M., / Guenther , S., / Turk , D., / Hinrichs , W., / Chapman , H.N., / Pearson , A., / Betzel , C., / Meents , A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 135.1 KB | Display | ![]() |
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PDB format | ![]() | 105.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ynqSC ![]() 6yvfC ![]() 7a1uC ![]() 7abuC ![]() 7adwC ![]() 7af0C ![]() 7agaC ![]() 7ahaC ![]() 7ak4C ![]() 7akuC ![]() 7amjC ![]() 7ansC ![]() 7aolC ![]() 7ap6C ![]() 7aphC ![]() 7aqeC ![]() 7aqiC ![]() 7aqjC ![]() 7ar5C ![]() 7ar6C ![]() 7arfC ![]() 7avdC ![]() 7awrC ![]() 7awsC ![]() 7awuC ![]() 7awwC ![]() 7axmC ![]() 7axoC ![]() 7ay7C ![]() 7b83C ![]() 7nevC 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 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.) ![]() ![]() Gene: rep, 1a-1b / Production host: ![]() ![]() References: UniProt: P0DTD1, SARS coronavirus main proteinase | ||||||
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#2: Chemical | ChemComp-S8H / ( | ||||||
#3: Chemical | #4: Chemical | ChemComp-IMD / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 / Details: 25% peg 1500, 5% dmso, 0.1 M MIB |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.888→47.73 Å / Num. obs: 20491 / % possible obs: 98.27 % / Redundancy: 3.8 % / Biso Wilson estimate: 35.5 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.27 |
Reflection shell | Resolution: 1.888→1.95 Å / Num. unique obs: 1745 / CC1/2: 0.495 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ynq Resolution: 1.95→47.73 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.15 / 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: 218.04 Å2 / Biso mean: 51.3242 Å2 / Biso min: 19 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→47.73 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %
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