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Yorodumi- PDB-2z3d: A Mechanistic view of Enzyme Inhibition and Peptide Hydrolysis in... -
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-Basic information
Entry | Database: PDB / ID: 2z3d | ||||||
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Title | A Mechanistic view of Enzyme Inhibition and Peptide Hydrolysis in the Active Site of the SARS-CoV 3C-Like peptidase | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / BETA BARRELS / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / : / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / endopeptidase complex ...viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / : / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / endopeptidase complex / endoribonuclease complex / : / mRNA capping enzyme complex / suppression by virus of host type I interferon production / positive stranded viral RNA replication / positive regulation of RNA biosynthetic process / protein K48-linked deubiquitination / : / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / protein K63-linked deubiquitination / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / RNA-templated transcription / viral transcription / SARS-CoV-1 modulates host translation machinery / protein autoprocessing / 7-methylguanosine mRNA capping / positive regulation of viral genome replication / DNA helicase activity / Transferases; Transferring one-carbon groups; Methyltransferases / helicase activity / protein processing / symbiont-mediated suppression of host gene expression / SARS-CoV-1 activates/modulates innate immune responses / double-stranded RNA binding / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / ISG15-specific peptidase activity / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / host cell cytoplasm / cysteine-type deubiquitinase activity / membrane => GO:0016020 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / protein dimerization activity / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / 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 / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | SARS coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Yin, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: A mechanistic view of enzyme inhibition and peptide hydrolysis in the active site of the SARS-CoV 3C-like peptidase Authors: Yin, J. / Niu, C. / Cherney, M.M. / Zhang, J. / Huitema, C. / Eltis, L.D. / 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 | 2z3d.cif.gz | 81.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z3d.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 2z3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z3d_validation.pdf.gz | 441.6 KB | Display | wwPDB validaton report |
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Full document | 2z3d_full_validation.pdf.gz | 445.2 KB | Display | |
Data in XML | 2z3d_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 2z3d_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/2z3d ftp://data.pdbj.org/pub/pdb/validation_reports/z3/2z3d | HTTPS FTP |
-Related structure data
Related structure data | 2z3cC 2z3eC 2a5aS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 33876.637 Da / Num. of mol.: 1 Fragment: UNP residues 3241-3546, SARS-CoV 3C-like peptidase Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Gene: rep / Plasmid: PT7HSP2 / Production host: Escherichia coli (E. coli) / Strain (production host): GJ1158 References: UniProt: P59641, UniProt: P0C6X7*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Protein/peptide | |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Compound details | THE INHIBITOR (CHAIN I) IS A MIXTURE OF A THIOACYL AND EPISULFIDE FORMS. THE UNBOUND FORM OF THE ...THE INHIBITOR (CHAIN I) IS A MIXTURE OF A THIOACYL AND EPISULFIDE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.38 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 50mM ammonium acetate, 5% polyethylene glycol (Mr10, 000), 3% ethylene glycol, 3% dimethyl sulfoxide, 1mM dithiothreitol, 0.1mM Mes (pH6.5) , VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.97946 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 5, 2006 / Details: crystal |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→64.55 Å / Num. all: 26214 / Num. obs: 23907 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.1→2.21 Å / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 5.1 / Num. unique all: 3821 / Rsym value: 0.328 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2A5A Resolution: 2.1→18.43 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 11.375 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.207 / ESU R Free: 0.189 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.552 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→18.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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