[English] 日本語
Yorodumi- PDB-3avz: Structure of SARS 3CL protease with peptidic aldehyde inhibitor c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3avz | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of SARS 3CL protease with peptidic aldehyde inhibitor containing cyclohexyl side chain | ||||||
Components |
| ||||||
Keywords | HYDROLASE/HYDROLASE inhibitor / HYDROLASE 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 / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / 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 / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / 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 / methylation / 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 / 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 / induction by virus of host autophagy / symbiont-mediated suppression of host gene expression / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / proteolysis / zinc ion binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | SARS coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3avz.cif.gz | 73.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3avz.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 3avz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/3avz ftp://data.pdbj.org/pub/pdb/validation_reports/av/3avz | HTTPS FTP |
---|
-Related structure data
Related structure data | 3atwC 3aw0C 3aw1C 2zu5S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33832.602 Da / Num. of mol.: 1 / 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.36 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 9-11%(w/v) PEG 20000, 100mM MES pH 6.0, 5mM DTT , VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jan 27, 2010 |
Radiation | Monochromator: Triangular with an asymmetric angle of 7.8 degree Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→50 Å / Num. obs: 15377 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 16.736 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.526 / Rsym value: 0.487 / % possible all: 83.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZU5 Resolution: 2.46→43.45 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.281 / SU ML: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 63.18 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.46→43.45 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.463→2.527 Å / Total num. of bins used: 20
|