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Yorodumi- PDB-6xhl: Covalent complex of SARS-CoV main protease with N-[(2S)-1-({(2S,3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xhl | |||||||||
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Title | Covalent complex of SARS-CoV main protease with N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide | |||||||||
Components | 3C-like proteinase | |||||||||
Keywords | VIRAL PROTEIN / coronavirus protease inhibitor complex | |||||||||
Function / homology | Function and homology information Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral genome replication ...Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral genome replication / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / 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 / 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 / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / proteolysis / zinc ion binding / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | Human SARS coronavirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.471 Å | |||||||||
Authors | Gajiwala, K.S. / Ferre, R.A. / Ryan, K. / Stewart, A.E. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Discovery of Ketone-Based Covalent Inhibitors of Coronavirus 3CL Proteases for the Potential Therapeutic Treatment of COVID-19. Authors: Hoffman, R.L. / Kania, R.S. / Brothers, M.A. / Davies, J.F. / Ferre, R.A. / Gajiwala, K.S. / He, M. / Hogan, R.J. / Kozminski, K. / Li, L.Y. / Lockner, J.W. / Lou, J. / Marra, M.T. / ...Authors: Hoffman, R.L. / Kania, R.S. / Brothers, M.A. / Davies, J.F. / Ferre, R.A. / Gajiwala, K.S. / He, M. / Hogan, R.J. / Kozminski, K. / Li, L.Y. / Lockner, J.W. / Lou, J. / Marra, M.T. / Mitchell Jr., L.J. / Murray, B.W. / Nieman, J.A. / Noell, S. / Planken, S.P. / Rowe, T. / Ryan, K. / Smith 3rd, G.J. / Solowiej, J.E. / Steppan, C.M. / Taggart, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xhl.cif.gz | 137.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xhl.ent.gz | 106.5 KB | Display | PDB format |
PDBx/mmJSON format | 6xhl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xhl_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6xhl_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6xhl_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 6xhl_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/6xhl ftp://data.pdbj.org/pub/pdb/validation_reports/xh/6xhl | HTTPS FTP |
-Related structure data
Related structure data | 6xhmC 6xhnC 6xhoC 1uk3S 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: 33933.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide Source: (gene. exp.) Human SARS coronavirus / Gene: 1a / Production host: Escherichia coli (E. coli) References: UniProt: P0C6U8, SARS coronavirus main proteinase #2: Chemical | #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: 2.31 Å3/Da / Density % sol: 46.74 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion Details: Precipitant: 10.0 %w/v (8.0 uL of stock 50.0 %w/v) PEG 6000; Buffer: 0.1 M (4.0 uL of stock 1.0 M) MES (pH 6.00); Additive: 0.0 %v/v (0.0 uL of stock 100.0 %v/v) Dimethyl sulfoxide; Additive: ...Details: Precipitant: 10.0 %w/v (8.0 uL of stock 50.0 %w/v) PEG 6000; Buffer: 0.1 M (4.0 uL of stock 1.0 M) MES (pH 6.00); Additive: 0.0 %v/v (0.0 uL of stock 100.0 %v/v) Dimethyl sulfoxide; Additive: 10.0 % w/v (5.0 uL of stock 80.0 % w/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 98 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 16, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.471→56.6 Å / Num. obs: 76744 / % possible obs: 74.2 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.03 / Rrim(I) all: 0.056 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.471→1.599 Å / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3839 / CC1/2: 0.543 / Rpim(I) all: 0.488 / Rrim(I) all: 0.777 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UK3 Resolution: 1.471→56.61 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.099 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.1 / SU Rfree Blow DPI: 0.093 / SU Rfree Cruickshank DPI: 0.093
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Displacement parameters | Biso mean: 26.67 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.471→56.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.471→1.55 Å
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