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Yorodumi- PDB-8e6c: Crystal structure of MERS 3CL protease in complex with a m-fluoro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8e6c | |||||||||
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Title | Crystal structure of MERS 3CL protease in complex with a m-fluorophenyl dimethyl sulfane inhibitor | |||||||||
Components | Orf1a protein | |||||||||
Keywords | HYDROLASE / Viral protein/Inhibitor / PROTEASE / protease Inhhibitors / Viral protein-Inhibitor complex | |||||||||
Function / homology | Function and homology information host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity ...host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / proteolysis / zinc ion binding / membrane Similarity search - Function | |||||||||
Biological species | Middle East respiratory syndrome-related coronavirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | |||||||||
Authors | Liu, L. / Lovell, S. / Battaile, K.P. / Dampalla, C.S. / Groutas, W.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2023 Title: Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and ...Title: Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV). Authors: Dampalla, C.S. / Miller, M.J. / Kim, Y. / Zabiegala, A. / Nguyen, H.N. / Madden, T.K. / Thurman, H.A. / Machen, A.J. / Cooper, A. / Liu, L. / Battaile, K.P. / Lovell, S. / Chang, K.O. / Groutas, W.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8e6c.cif.gz | 130.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8e6c.ent.gz | 99.3 KB | Display | PDB format |
PDBx/mmJSON format | 8e6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8e6c_validation.pdf.gz | 705.9 KB | Display | wwPDB validaton report |
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Full document | 8e6c_full_validation.pdf.gz | 706.9 KB | Display | |
Data in XML | 8e6c_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 8e6c_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/8e6c ftp://data.pdbj.org/pub/pdb/validation_reports/e6/8e6c | HTTPS FTP |
-Related structure data
Related structure data | 8e5xC 8e5zC 8e61C 8e63C 8e64C 8e65C 8e68C 8e69C 8e6aC 8e6bC 8e6dC 8e6eC 8f44C 8f45C 8f46C 5wkkS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34314.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus Gene: orf1a / Plasmid: PET28 / Cell (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L2E0X0 |
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#2: Chemical | ChemComp-UTU / [ |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% (w/v) PEG 3350, 100 mM Tris, 200 mM magnesium chloride |
-Data collection
Diffraction | Mean temperature: 291 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jun 6, 2022 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→48.89 Å / Num. obs: 7324 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 44.47 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.093 / Rrim(I) all: 0.174 / Net I/σ(I): 5.3 / Num. measured all: 25099 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WKK Resolution: 2.7→46.66 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.12 Å2 / Biso mean: 45.8168 Å2 / Biso min: 21.26 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→46.66 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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