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Yorodumi- PDB-2h6m: An episulfide cation (thiiranium ring) trapped in the active site... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h6m | ||||||
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Title | An episulfide cation (thiiranium ring) trapped in the active site of HAV 3C proteinase inactivated by peptide-based ketone inhibitors | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / BETA BARREL / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity ...host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / 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 / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Hepatitis A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Yin, J. / Cherney, M.M. / Bergmann, E.M. / James, M.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: An episulfide cation (thiiranium ring) trapped in the active site of HAV 3C proteinase inactivated by peptide-based ketone inhibitors. Authors: Yin, J. / Cherney, M.M. / Bergmann, E.M. / Zhang, J. / Huitema, C. / Pettersson, H. / Eltis, L.D. / Vederas, J.C. / James, M.N. #1: Journal: J.Mol.Biol. / Year: 2005 Title: Dual Modes of Modification of Hepatitis A Virus 3C Protease by a Serine-derived beta-lactone: selective crystallization and formation of a functional catalytic triad in the active site Authors: Yin, J. / Bergmann, E.M. / Cherney, M.M. / Lall, M.S. / Jain, R.P. / Vederas, J.C. / James, M.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h6m.cif.gz | 59.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h6m.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 2h6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h6m_validation.pdf.gz | 451.5 KB | Display | wwPDB validaton report |
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Full document | 2h6m_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 2h6m_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 2h6m_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/2h6m ftp://data.pdbj.org/pub/pdb/validation_reports/h6/2h6m | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | biological assembly is a monomer |
-Components
#1: Protein | Mass: 23288.844 Da / Num. of mol.: 1 / Mutation: C24S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis A virus / Genus: Hepatovirus / Gene: 3C gene / Plasmid: pHAV-3CEX / Production host: Escherichia coli (E. coli) / Strain (production host): D1210 References: UniProt: P06441, UniProt: P08617*PLUS, picornain 3C |
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#2: Protein/peptide | |
#3: Chemical | ChemComp-BBL / |
#4: Water | ChemComp-HOH / |
Compound details | THE UNBOUND FORM OF THE INHIBITOR IS N-ACETYL-LEUCYL-ALANYL-ALANYL-(N,N-DIMETHYL)-GLUTAMINE-(1,4- ...THE UNBOUND FORM OF THE INHIBITOR IS N-ACETYL-LEUCYL-ALANYL-ALANYL-(N,N-DIMETHYL)-GLUTAMINE-(1,4-DIOXO-3,4-DIHYDRO-1H-PHTHALAZIN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.83 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.5% PEG 8000, 1.5% Glycerol, 10mM Tris-HCl pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 29, 2004 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1159 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→46.08 Å / Num. all: 38782 / Num. obs: 38520 / % possible obs: 75.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.068 |
Reflection shell | Resolution: 1.4→1.45 Å / % possible all: 79.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→46.08 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.386 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.362 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→46.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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