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Yorodumi- PDB-3mj5: Severe Acute Respiratory Syndrome-Coronavirus Papain-Like Proteas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mj5 | ||||||
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Title | Severe Acute Respiratory Syndrome-Coronavirus Papain-Like Protease Inhibitors: Design, Synthesis, Protein-Ligand X-ray Structure and Biological Evaluation | ||||||
Components | Replicase polyprotein 1a | ||||||
Keywords | VIRAL PROTEIN / non-covalent inhibitor / cysteine protease / SARS coronavirus / zinc-finger | ||||||
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: 2.63 Å | ||||||
Authors | Mesecar, A.D. / Ratia, K.M. / Pegan, S.D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2010 Title: Severe acute respiratory syndrome coronavirus papain-like novel protease inhibitors: design, synthesis, protein-ligand X-ray structure and biological evaluation Authors: Ghosh, A.K. / Takayama, J. / Rao, K.V. / Ratia, K. / Chaudhuri, R. / Mulhearn, D.C. / Lee, H. / Nichols, D.B. / Baliji, S. / Baker, S.C. / Johnson, M.E. / Mesecar, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mj5.cif.gz | 128.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mj5.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 3mj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/3mj5 ftp://data.pdbj.org/pub/pdb/validation_reports/mj/3mj5 | HTTPS FTP |
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-Related structure data
Related structure data | 2fe8S 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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2 |
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3 |
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Unit cell |
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Details | Monomer of PLpro bound to inhibitor |
-Components
#1: Protein | Mass: 35520.273 Da / Num. of mol.: 2 / Fragment: SARS polyprotein residues 1544-1855 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Strain: Urbani / Gene: 1a, ORF1 (nsp3) residues 1544-1855 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0C6U8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Chemical | #3: Chemical | #4: 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: 2.92 Å3/Da / Density % sol: 57.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Diffraction-quality crystals grew from a sitting drop containing 5 mg/mL PLpro, 1 mM inhibitor, 1 M (NH4)2SO4, 50 mM MES, pH 6.5, and 2.5% PEG 400., VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 16, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. all: 24417 / Num. obs: 23605 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 3.37 % / Biso Wilson estimate: 61.6 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.18 / Num. unique all: 2025 / % possible all: 85.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2FE8 Resolution: 2.63→94.42 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.911 / SU B: 8.816 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.066 / 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: 49.977 Å2
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Refinement step | Cycle: LAST / Resolution: 2.63→94.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.633→2.701 Å / Total num. of bins used: 20
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