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Yorodumi- PDB-8dgy: Structure of MERS 3CL protease in complex with the cyclopropane b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dgy | |||||||||
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Title | Structure of MERS 3CL protease in complex with the cyclopropane based inhibitor 16d (high resolution) | |||||||||
Components | 3C-like proteinase | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / PROTEASE / severe acute respiratory syndrome coronavirus 2 / MERS 3CL protease Inhhibitors / hydrolase / HYDROLASE-HYDROLASE 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 / symbiont-mediated perturbation of host ubiquitin-like protein modification / methylation / 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 / symbiont-mediated perturbation of host ubiquitin-like protein modification / methylation / 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: 1.65 Å | |||||||||
Authors | Lovell, S. / Liu, L. / Battaile, K.P. / Nguyen, H.N. / Chamandi, S.D. / Picard, H.R. / Madden, T.K. / Thruman, H.A. / Kim, Y. / Groutas, W.C. / Chang, K.O. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Acs Pharmacol Transl Sci / Year: 2023 Title: Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies. Authors: Dampalla, C.S. / Nguyen, H.N. / Rathnayake, A.D. / Kim, Y. / Perera, K.D. / Madden, T.K. / Thurman, H.A. / Machen, A.J. / Kashipathy, M.M. / 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 | 8dgy.cif.gz | 80.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dgy.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 8dgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dgy_validation.pdf.gz | 936.7 KB | Display | wwPDB validaton report |
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Full document | 8dgy_full_validation.pdf.gz | 937.1 KB | Display | |
Data in XML | 8dgy_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 8dgy_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/8dgy ftp://data.pdbj.org/pub/pdb/validation_reports/dg/8dgy | HTTPS FTP |
-Related structure data
Related structure data | 7tq2C 7tq3C 7tq4C 7tq5C 7tq6C 7tq7C 7tq8C 8cztC 8czuC 8czvC 8czwC 8czxC 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 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A1L2E0X0 |
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#2: Chemical | ChemComp-S9U / [( |
#3: Chemical | ChemComp-SD6 / [( |
#4: 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: 1.98 Å3/Da / Density % sol: 37.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.8 M Potassium sodium tartrate tetrahydrate, 100 mM Tris, 0.5% (w/v) Polyethylene glycol monomethyl ether 5,000 |
-Data collection
Diffraction | Mean temperature: 100 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 | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.65→49.33 Å / Num. obs: 31215 / % possible obs: 96.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 22.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.9 / Num. measured all: 113311 | ||||||||||||||||||||||||
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: 1.65→24.53 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.05 / Phase error: 20.98 / 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: 88.8 Å2 / Biso mean: 27.7372 Å2 / Biso min: 12.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→24.53 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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