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Yorodumi- PDB-9ata: Crystal structure of MERS 3CL protease in complex with a phenylet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9ata | |||||||||
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Title | Crystal structure of MERS 3CL protease in complex with a phenylethyl 2-pyrrolidone inhibitor | |||||||||
Components | 3C-like proteinase nsp5 | |||||||||
Keywords | HYDROLASE/INHIBITOR / MERS / 3CL protease inhibitors / COVID-19 / viral protein / HYDROLASE-INHIBITOR complex | |||||||||
Function / homology | Function and homology information 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 | Middle East respiratory syndrome-related coronavirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Liu, L. / Lovell, S. / Battaile, K.P. / Dampalla, C.S. / Groutas, W.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Med.Chem. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9ata.cif.gz | 259.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9ata.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9ata.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9ata_validation.pdf.gz | 805.2 KB | Display | wwPDB validaton report |
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Full document | 9ata_full_validation.pdf.gz | 806 KB | Display | |
Data in XML | 9ata_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 9ata_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/9ata ftp://data.pdbj.org/pub/pdb/validation_reports/at/9ata | HTTPS FTP |
-Related structure data
Related structure data | 9asvC 9aswC 9asyC 9aszC 9at0C 9at1C 9at3C 9at4C 9at5C 9at6C 9at7C 9atdC 9ateC 9atfC 9atgC 9athC 9atiC 9atjC 9atsC 9attC 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.: 2 / Fragment: UNP residues 3248-3553 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus Gene: 1a / Plasmid: pET-28 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: K9N638, SARS coronavirus main proteinase #2: Chemical | Mass: 596.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H40N4O9S #3: Chemical | Mass: 596.693 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C27H40N4O9S #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.85 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 30% w/v PEG2000 MME, 150 mM potassium bromide |
-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: 0.9795 Å |
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: 1.65→106.22 Å / Num. obs: 68424 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.025 / Rrim(I) all: 0.067 / Χ2: 0.99 / Net I/σ(I): 14.8 / Num. measured all: 470099 |
Reflection shell | Resolution: 1.65→1.69 Å / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.953 / Num. measured all: 35445 / Num. unique obs: 5024 / CC1/2: 0.741 / Rpim(I) all: 0.385 / Rrim(I) all: 1.029 / Χ2: 0.98 / Net I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→24.04 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.96 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→24.04 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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