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Yorodumi- PDB-5wkj: 2.05 A resolution structure of MERS 3CL protease in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wkj | ||||||
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Title | 2.05 A resolution structure of MERS 3CL protease in complex with inhibitor GC376 | ||||||
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: 2.05 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 | 5wkj.cif.gz | 81.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wkj.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 5wkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wkj_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5wkj_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5wkj_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 5wkj_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/5wkj ftp://data.pdbj.org/pub/pdb/validation_reports/wk/5wkj | HTTPS FTP |
-Related structure data
Related structure data | 5wkkC 5wklC 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 | #3: Chemical | ChemComp-B1S / ( | #4: Chemical | ChemComp-K36 / ( | #5: Water | ChemComp-HOH / | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% (v/v) PEG 550 MME, 100 mM Bis-Tris, 50 mM CaCl2 |
-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: Aug 16, 2015 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.05→49.57 Å / Num. obs: 16912 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 26.94 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.3 / Num. measured all: 56558 / Scaling rejects: 1 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RSP Resolution: 2.05→41.787 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.19 / Phase error: 25.56 / 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: 87.55 Å2 / Biso mean: 31.4912 Å2 / Biso min: 10.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.05→41.787 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: 6
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