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Open data
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Basic information
Entry | Database: PDB / ID: 7t41 | ||||||
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Title | Structure of MERS 3CL protease in complex with inhibitor 14c | ||||||
![]() | 3C-like proteinase | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / COVID-19 / PROTEASE / MERS 3CL protease Inhhibitors / hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() host cell membrane / viral genome replication / methyltransferase activity / SARS coronavirus main proteinase / 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 ...host cell membrane / viral genome replication / methyltransferase activity / SARS coronavirus main proteinase / 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 / 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 / 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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Lovell, S. / Kashipathy, M.M. / Battaile, K.P. / Chamandi, S.D. / Kim, Y. / Groutas, W.C. / Chang, K.O. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease. Authors: Dampalla, C.S. / Rathnayake, A.D. / Galasiti Kankanamalage, A.C. / Kim, Y. / Perera, K.D. / Nguyen, H.N. / Miller, M.J. / Madden, T.K. / Picard, H.R. / Thurman, H.A. / Kashipathy, M.M. / ...Authors: Dampalla, C.S. / Rathnayake, A.D. / Galasiti Kankanamalage, A.C. / Kim, Y. / Perera, K.D. / Nguyen, H.N. / Miller, M.J. / Madden, T.K. / Picard, H.R. / Thurman, H.A. / 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 | ![]() | 77.2 KB | Display | ![]() |
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PDB format | ![]() | 53.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 949.5 KB | Display | ![]() |
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Full document | ![]() | 963 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 19.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7t3yC ![]() 7t3zC ![]() 7t40C ![]() 7t42C ![]() 7t43C ![]() 7t44C ![]() 7t45C ![]() 7t46C ![]() 7t48C ![]() 7t49C ![]() 7t4aC ![]() 7t4bC ![]() 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
#1: Protein | Mass: 34314.242 Da / Num. of mol.: 1 / Fragment: Full Length Source method: isolated from a genetically manipulated source Details: N-terminal hexahistidine tag Source: (gene. exp.) ![]() Strain: isolate United Kingdom/H123990006/2012 / Gene: 1a / Plasmid: pET28 / Production host: ![]() ![]() References: UniProt: K9N638, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Chemical | ChemComp-FWI / ( |
#3: Chemical | ChemComp-FZI / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% (w/v) PEG 3350, 100 mM Hepes, 200 mM magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2021 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.1→46.96 Å / Num. obs: 15305 / % possible obs: 97.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 28.65 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.122 / Net I/σ(I): 7.9 / Num. measured all: 50969 / Scaling rejects: 20 | ||||||||||||||||||||||||
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: 2.1→37.55 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.05 / Phase error: 25.3 / 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: 33.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→37.55 Å
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LS refinement shell |
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