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Yorodumi- PDB-5gwy: Structure of Main Protease from Human Coronavirus NL63: Insights ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gwy | |||||||||
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Title | Structure of Main Protease from Human Coronavirus NL63: Insights for Wide Spectrum Anti-Coronavirus Drug Design | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / HCoV-NL63 / Main protease / Inhibitor / Complex / Drug Design / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information host cell membrane / viral genome replication / transferase activity / 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 / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm ...host cell membrane / viral genome replication / transferase activity / 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 / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / proteolysis / RNA binding / zinc ion binding / membrane Similarity search - Function | |||||||||
Biological species | Human coronavirus NL63 synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.852 Å | |||||||||
Authors | Wang, F. / Chen, C. / Tan, W. / Yang, K. / Yang, H. | |||||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Structure of Main Protease from Human Coronavirus NL63: Insights for Wide Spectrum Anti-Coronavirus Drug Design. Authors: Wang, F. / Chen, C. / Tan, W. / Yang, K. / Yang, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gwy.cif.gz | 137.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gwy.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 5gwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gwy_validation.pdf.gz | 460.1 KB | Display | wwPDB validaton report |
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Full document | 5gwy_full_validation.pdf.gz | 470.6 KB | Display | |
Data in XML | 5gwy_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 5gwy_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/5gwy ftp://data.pdbj.org/pub/pdb/validation_reports/gw/5gwy | HTTPS FTP |
-Related structure data
Related structure data | 3tloS 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: 33174.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human coronavirus NL63 / Gene: 1a / Production host: Escherichia coli (E. coli) References: UniProt: P0C6U6, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Protein/peptide | Type: Peptide-like / Class: Inhibitor / Mass: 680.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) References: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE #3: Water | ChemComp-HOH / | |
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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: 3 Å3/Da / Density % sol: 59.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M Sodium Citrate Tribasic dihydrate, 1.0 M Ammonium Phosphate Monobasie |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 19967 / % possible obs: 100 % / Redundancy: 14.2 % / Net I/σ(I): 21.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TLO Resolution: 2.852→46.483 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.852→46.483 Å
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Refine LS restraints |
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LS refinement shell |
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