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- PDB-7tq8: Structure of MERS 3CL protease in complex with the cyclopropane b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tq8 | ||||||
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Title | Structure of MERS 3CL protease in complex with the cyclopropane based inhibitor 14d | ||||||
![]() | Orf1a protein | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / PROTEASE / severe acute respiratory syndrome coronavirus 2 / MERS 3CL protease Inhhibitors / hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, L. / Lovell, S. / 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 | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.6 KB | Display | ![]() |
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PDB format | ![]() | 57.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tq2C ![]() 7tq3C ![]() 7tq4C ![]() 7tq5C ![]() 7tq6C ![]() 7tq7C ![]() 8cztC ![]() 8czuC ![]() 8czvC ![]() 8czwC ![]() 8czxC ![]() 8dgyC ![]() 5wkkS 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: 34314.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: orf1a / Plasmid: pET28 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-IRK / ( |
#3: Chemical | ChemComp-IUB / ( |
#4: Chemical | ChemComp-PG4 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% (w/v) PEG 3350, 100 mM Tris, 200 mM Lithium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→49.01 Å / Num. obs: 31177 / % possible obs: 98.2 % / Redundancy: 5.2 % / Biso Wilson estimate: 21.12 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.777 / Num. unique obs: 1431 / % possible all: 94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5WKK Resolution: 1.65→46.05 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.02 / Phase error: 20.2 / 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 mean: 25.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→46.05 Å
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LS refinement shell |
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