+Open data
-Basic information
Entry | Database: PDB / ID: 2zu3 | ||||||
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Title | Complex structure of CVB3 3C protease with TG-0204998 | ||||||
Components | 3C proteinase | ||||||
Keywords | hydrolase/hydrolase inhibitor / protease-inhibitor complex / Hydrolase / Thiol protease / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host transcription / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host transcription / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / host cell cytoplasm / RNA helicase activity / symbiont entry into host cell / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / nucleotide binding / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Human coxsackievirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Lee, C.C. / Tsui, Y.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 | 2zu3.cif.gz | 56.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zu3.ent.gz | 39.1 KB | Display | PDB format |
PDBx/mmJSON format | 2zu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/2zu3 ftp://data.pdbj.org/pub/pdb/validation_reports/zu/2zu3 | HTTPS FTP |
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-Related structure data
Related structure data | 2ztxSC 2ztyC 2ztzC 2zu1C 2zu2C 2zu4C 2zu5C 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20298.293 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human coxsackievirus / Strain: B3 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) References: UniProt: Q90092, UniProt: P03313*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Chemical | ChemComp-ZU3 / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | THE UNBOUND VERSION OF THE INHIBITOR HAS A DOUBLE BOND BETWEEN ATOMS C63 AND C82, WHICH OPENS UP ...THE UNBOUND VERSION OF THE INHIBITOR HAS A DOUBLE BOND BETWEEN ATOMS C63 AND C82, WHICH OPENS UP WHEN IT COVALENTLY |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.39 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 24~30% PEG 4000, 0.2M magnesium chloride, 0.1M Tris-HCl , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 286K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 25, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 17634 / Num. obs: 17369 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2 / Num. unique all: 1718 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZTX Resolution: 1.75→25.03 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 86.849 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 82.47 Å2 / Biso mean: 34.23 Å2 / Biso min: 17.47 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→25.03 Å
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Refine LS restraints |
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