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- PDB-9atd: Crystal structure of MERS 3CL protease in complex with a ethylcyc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9atd | |||||||||
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Title | Crystal structure of MERS 3CL protease in complex with a ethylcyclohexyl 2-pyrrolidone inhibitor (S-enantiomer) inhibitor | |||||||||
![]() | 3C-like proteinase nsp5 | |||||||||
![]() | HYDROLASE/INHIBITOR / MERS / 3CL protease inhibitors / COVID-19 / viral protein / 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 / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / methylation / 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 | ![]() ![]() ![]() | |||||||||
![]() | Liu, L. / Lovell, S. / Battaile, K.P. / Dampalla, C.S. / Groutas, W.C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Guided Design of Potent Coronavirus Inhibitors with a 2-Pyrrolidone Scaffold: Biochemical, Crystallographic, and Virological Studies. Authors: Dampalla, C.S. / Kim, Y. / Zabiegala, A. / Howard, D.J. / Nguyen, H.N. / Madden, T.K. / Thurman, H.A. / 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 991.5 KB | Display | ![]() |
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Full document | ![]() | 992 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 21.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9asvC ![]() 9aswC ![]() 9asyC ![]() 9aszC ![]() 9at0C ![]() 9at1C ![]() 9at3C ![]() 9at4C ![]() 9at5C ![]() 9at6C ![]() 9at7C ![]() 9ataC ![]() 9ateC ![]() 9atfC ![]() 9atgC ![]() 9athC ![]() 9atiC ![]() 9atjC ![]() 9atsC ![]() 9attC 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
#1: Protein | Mass: 34314.242 Da / Num. of mol.: 1 / Fragment: UNP residues 3248-3553 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: 1a / Plasmid: pET-28 / Production host: ![]() ![]() References: UniProt: K9N638, SARS coronavirus main proteinase |
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#2: Chemical | ChemComp-A1AGL / ( Mass: 602.741 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46N4O9S |
#3: Chemical | ChemComp-A1AGK / ( Mass: 602.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C27H46N4O9S |
#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: 37.48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% w/v PEG3350, 100 mM Bis-Tris, pH 5.5, 200 mM ammonium acetate |
-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: Oct 5, 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: 1.8→49.16 Å / Num. obs: 24796 / % possible obs: 99.9 % / Redundancy: 4.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.035 / Rrim(I) all: 0.079 / Χ2: 0.96 / Net I/σ(I): 11.7 / Num. measured all: 119312 |
Reflection shell | Resolution: 1.8→1.85 Å / % possible obs: 99.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.851 / Num. measured all: 8788 / Num. unique obs: 1825 / CC1/2: 0.68 / Rpim(I) all: 0.42 / Rrim(I) all: 0.952 / Χ2: 0.91 / Net I/σ(I) obs: 1.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→47.05 Å
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Refine LS restraints |
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LS refinement shell |
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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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