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Yorodumi- PDB-3sji: crystal structure of CVA16 3C in complex with Rupintrivir (AG7088) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sji | ||||||
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Title | crystal structure of CVA16 3C in complex with Rupintrivir (AG7088) | ||||||
Components | 3C proteasePicornain 3C | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / in complex with Rupintrivir / Chymotrypsin-like fold / protease / C147 covalently binds to Rupintrivir / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information T=pseudo3 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / proteolysis / RNA binding ...T=pseudo3 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / proteolysis / RNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Human coxsackievirus A16 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.798 Å | ||||||
Authors | Lu, G. / Qi, J. / Chen, Z. / Xu, X. / Gao, F. / Lin, D. / Qian, W. / Liu, H. / Jiang, H. / Yan, J. / Gao, G.F. | ||||||
Citation | Journal: J.Virol. / Year: 2011 Title: Enterovirus 71 and Coxsackievirus A16 3C Proteases: Binding to Rupintrivir and Their Substrates and Anti-Hand, Foot, and Mouth Disease Virus Drug Design. Authors: Lu, G. / Qi, J. / Chen, Z. / Xu, X. / Gao, F. / Lin, D. / Qian, W. / Liu, H. / Jiang, H. / Yan, J. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sji.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sji.ent.gz | 70.1 KB | Display | PDB format |
PDBx/mmJSON format | 3sji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/3sji ftp://data.pdbj.org/pub/pdb/validation_reports/sj/3sji | HTTPS FTP |
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-Related structure data
Related structure data | 3sj8SC 3sj9C 3sjkC 3sjoC 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: 21090.186 Da / Num. of mol.: 1 / Fragment: UNP residues 1-183 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human coxsackievirus A16 / Strain: Beijing0907 / Gene: 3C / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C8CIL7, picornain 3C |
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#2: Chemical | ChemComp-AG7 / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.36 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M sodium acetate, pH 4.6, 0.1 M magnesium chloride, 25% w/v PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Oct 26, 2010 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.798→50 Å / Num. all: 14740 / Num. obs: 14147 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.932 / Num. unique all: 1245 / Rsym value: 0.416 / % possible all: 86.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SJ8 Resolution: 1.798→28.571 Å / SU ML: 0.25 / σ(F): 0.12 / Phase error: 21.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.161 Å2 / ksol: 0.367 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.798→28.571 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Origin x: 0.2326 Å / Origin y: -19.2525 Å / Origin z: -2.767 Å
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Refinement TLS group | Selection details: all |