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Yorodumi- PDB-3atw: Structure-Based Design, Synthesis, Evaluation of Peptide-mimetic ... -
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-Basic information
Entry | Database: PDB / ID: 3atw | ||||||
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Title | Structure-Based Design, Synthesis, Evaluation of Peptide-mimetic SARS 3CL Protease Inhibitors | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / hydrase proteinase converting / designed inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / 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 / SARS-CoV-1 modulates host translation machinery / viral genome replication ...Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / 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 / SARS-CoV-1 modulates host translation machinery / viral genome replication / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / 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 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / methylation / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / proteolysis / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | SARS coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | ||||||
Authors | Akaji, K. / Konno, H. / Mitsui, H. / Teruya, K. / Hattori, Y. / Ozaki, T. / Kusunoki, M. / Sanjho, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: Structure-Based Design, Synthesis, and Evaluation of Peptide-Mimetic SARS 3CL Protease Inhibitors. Authors: Akaji, K. / Konno, H. / Mitsui, H. / Teruya, K. / Shimamoto, Y. / Hattori, Y. / Ozaki, T. / Kusunoki, M. / Sanjoh, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3atw.cif.gz | 133.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3atw.ent.gz | 103.1 KB | Display | PDB format |
PDBx/mmJSON format | 3atw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3atw_validation.pdf.gz | 443.5 KB | Display | wwPDB validaton report |
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Full document | 3atw_full_validation.pdf.gz | 447.8 KB | Display | |
Data in XML | 3atw_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 3atw_validation.cif.gz | 36.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/3atw ftp://data.pdbj.org/pub/pdb/validation_reports/at/3atw | HTTPS FTP |
-Related structure data
Related structure data | 3avzC 3aw0C 3aw1C 2zu5S 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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Unit cell |
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-Components
#1: Protein | Mass: 33832.602 Da / Num. of mol.: 2 / Mutation: R188I Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Gene: 1a / Plasmid: pMAL-3CL-R188I / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0C6U8, SARS coronavirus main proteinase #2: Protein/peptide | #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: 2.89 Å3/Da / Density % sol: 57.44 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 9-11%(w/v) of PEG 20000, 100mM MES pH 6.0, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: May 23, 2009 |
Radiation | Monochromator: Triangular with an asymmetric angle of 7.8 A / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 31735 / Num. obs: 31735 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.36→2.4 Å / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2409 / % possible all: 77.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZU5 Resolution: 2.36→46.4 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / SU B: 7.049 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.242 / 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: 33.738 Å2
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Refinement step | Cycle: LAST / Resolution: 2.36→46.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.353→2.414 Å / Total num. of bins used: 20
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