+Open data
-Basic information
Entry | Database: PDB / ID: 6l70 | ||||||
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Title | Complex structure of PEDV 3CLpro with GC376 | ||||||
Components | PEDV main protease | ||||||
Keywords | HYDROLASE / 3C-Like Protease / complex | ||||||
Function / homology | Function and homology information host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / viral genome replication / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / mRNA (nucleoside-2'-O-)-methyltransferase activity / endonuclease activity ...host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / viral genome replication / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / mRNA (nucleoside-2'-O-)-methyltransferase activity / endonuclease activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Porcine epidemic diarrhea virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å | ||||||
Authors | Ye, G. / Peng, G.Q. | ||||||
Citation | Journal: Viruses / Year: 2020 Title: Structural Basis for Inhibiting Porcine Epidemic Diarrhea Virus Replication with the 3C-Like Protease Inhibitor GC376. Authors: Ye, G. / Wang, X. / Tong, X. / Shi, Y. / Fu, Z.F. / Peng, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l70.cif.gz | 230.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l70.ent.gz | 186.1 KB | Display | PDB format |
PDBx/mmJSON format | 6l70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/6l70 ftp://data.pdbj.org/pub/pdb/validation_reports/l7/6l70 | HTTPS FTP |
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-Related structure data
Related structure data | 4xfqS S: Starting model for refinement |
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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
#1: Protein | Mass: 33295.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porcine epidemic diarrhea virus / Gene: Pol1 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: K4L9I6 #2: Chemical | #3: 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: 2.26 Å3/Da / Density % sol: 45.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1 M NaCl, 0.2 M Na2HPO4, citric acid (pH 4.2), 5% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→57.2 Å / Num. obs: 90828 / % possible obs: 98.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.51→1.59 Å / Rmerge(I) obs: 0.705 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 13354 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XFQ Resolution: 1.56→39.804 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 117.95 Å2 / Biso mean: 32.0803 Å2 / Biso min: 14.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.56→39.804 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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