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- PDB-8czv: 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: 8czv | |||||||||
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Title | Structure of MERS 3CL protease in complex with the cyclopropane based inhibitor 17d | |||||||||
![]() | 3C-like proteinase | |||||||||
![]() | 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 | ![]() | 133.9 KB | Display | ![]() |
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PDB format | ![]() | 99.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1004.9 KB | Display | ![]() |
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Full document | ![]() | 1007 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tq2C ![]() 7tq3C ![]() 7tq4C ![]() 7tq5C ![]() 7tq6C ![]() 7tq7C ![]() 7tq8C ![]() 8cztC ![]() 8czuC ![]() 8czwC ![]() 8czxC ![]() 8dgyC ![]() 5wkkS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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-P8C / [( |
#3: Chemical | ChemComp-PJR / [( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% (w/v) PEG 3350, 100 mM Bis-Tris, 200 mM Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 24, 2022 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.95→48.99 Å / Num. obs: 19345 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 26.02 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.8 / Num. measured all: 68418 / Scaling rejects: 23 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5WKK Resolution: 1.95→48.99 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 31.19 / 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: 97.19 Å2 / Biso mean: 35.228 Å2 / Biso min: 18.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→48.99 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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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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