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Yorodumi- PDB-5wkl: 1.85 A resolution structure of MERS 3CL protease in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wkl | ||||||
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Title | 1.85 A resolution structure of MERS 3CL protease in complex with piperidine-based peptidomimetic inhibitor 17 | ||||||
Components | Orf1a protein | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / PROTEASE / protease Inhhibitors / HYDROLASE / HYDROLASE-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 / host cell perinuclear region of cytoplasm / single-stranded RNA binding / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral translational frameshifting / 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 / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Lovell, S. / Battaile, K.P. / Mehzabeen, N. / Kankanamalage, A.C.G. / Kim, Y. / Rathnayake, A.D. / Chang, K.O. / Groutas, W.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Eur J Med Chem / Year: 2018 Title: Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element. Authors: Galasiti Kankanamalage, A.C. / Kim, Y. / Damalanka, V.C. / Rathnayake, A.D. / Fehr, A.R. / Mehzabeen, N. / Battaile, K.P. / Lovell, S. / Lushington, G.H. / Perlman, 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 | 5wkl.cif.gz | 79.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wkl.ent.gz | 54.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wkl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wkl_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5wkl_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5wkl_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 5wkl_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/5wkl ftp://data.pdbj.org/pub/pdb/validation_reports/wk/5wkl | HTTPS FTP |
-Related structure data
Related structure data | 5wkjC 5wkkC 5wkmC 4rspS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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 / Fragment: Peptidase C30 domain residues 3248-3553 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus Gene: orf1a / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A1L2E0X0, UniProt: K9N638*PLUS |
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#2: Chemical | ChemComp-AVY / ( |
#3: Chemical | ChemComp-B3J / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25% (w/v) PEG 3350, 100 mM Bis-Tris, 200 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2016 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.85→46.94 Å / Num. obs: 22772 / % possible obs: 99.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 22.32 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.3 | ||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.2 %
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RSP Resolution: 1.85→46.938 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 22.5
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.38 Å2 / Biso mean: 28.4508 Å2 / Biso min: 10.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→46.938 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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