+Open data
-Basic information
Entry | Database: PDB / ID: 2zu2 | ||||||
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Title | complex structure of CoV 229E 3CL protease with EPDTC | ||||||
Components | 3C-like proteinase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / protease-inhibitor complex / Hydrolase / Metal-binding / Protease / Thiol protease / 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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Lee, C.C. / Wang, A.H.-J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structural Basis of Inhibition Specificities of 3C and 3C-like Proteases by Zinc-coordinating and Peptidomimetic Compounds Authors: Lee, C.C. / Kuo, C.J. / Ko, T.P. / Hsu, M.F. / Tsui, Y.C. / Chang, S.C. / Yang, S. / Chen, S.J. / Chen, H.C. / Hsu, M.C. / Shih, S.R. / Liang, P.H. / Wang, A.H.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zu2.cif.gz | 136.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zu2.ent.gz | 105.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zu2_validation.pdf.gz | 457.2 KB | Display | wwPDB validaton report |
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Full document | 2zu2_full_validation.pdf.gz | 467.9 KB | Display | |
Data in XML | 2zu2_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 2zu2_validation.cif.gz | 42.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/2zu2 ftp://data.pdbj.org/pub/pdb/validation_reports/zu/2zu2 | HTTPS FTP |
-Related structure data
Related structure data | 2ztxC 2ztyC 2ztzC 2zu1C 2zu3C 2zu4C 2zu5C 1p9sS C: citing same article (ref.) 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: 33083.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human coronavirus / Strain: 229E / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) References: UniProt: P0C6U2, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Chemical | ChemComp-MPD / ( | #3: Chemical | #4: 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: 2.38 Å3/Da / Density % sol: 48.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 18% PEG 6000, 10% DMSO, 14% MPD, 0.1M Tris-HCL, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 19, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 57371 / Num. obs: 57142 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2.91 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P9S Resolution: 1.8→34.34 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 5161
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Solvent computation | Bsol: 46.133 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.03 Å2 / Biso mean: 26.006 Å2 / Biso min: 7.81 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→34.34 Å
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Refine LS restraints |
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