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Yorodumi- PDB-3zzb: Crystal structure of 3C protease of coxsackievirus B3 complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zzb | ||||||
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Title | Crystal structure of 3C protease of coxsackievirus B3 complexed with alpha, beta-unsaturated ethyl ester inhibitor 85 | ||||||
Components | 3C PROTEINASE | ||||||
Keywords | HYDROLASE / PICORNAVIRIDAE | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / host cell cytoplasm / DNA replication / RNA helicase activity / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / nucleotide binding / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | HUMAN COXSACKIEVIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Tan, J. / Anand, K. / Mesters, J.R. / Hilgenfeld, R. | ||||||
Citation | Journal: To be Published Title: Peptidic Alpha, Beta-Unsaturated Ethyl Esters as Inhibitors of the 3C Protease of Coxsackie Virus B3: Crystal Structures, Antiviral Activities, and Resistance Mutations Authors: Tan, J. / Anand, K. / Mesters, J.R. / Hilgenfeld, R. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zzb.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zzb.ent.gz | 36.2 KB | Display | PDB format |
PDBx/mmJSON format | 3zzb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zzb_validation.pdf.gz | 733.5 KB | Display | wwPDB validaton report |
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Full document | 3zzb_full_validation.pdf.gz | 735.3 KB | Display | |
Data in XML | 3zzb_validation.xml.gz | 10 KB | Display | |
Data in CIF | 3zzb_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/3zzb ftp://data.pdbj.org/pub/pdb/validation_reports/zz/3zzb | HTTPS FTP |
-Related structure data
Related structure data | 3zyeC 3zz3C 3zz4C 3zz5C 3zz7C 3zz8C 3zz9C 3zzaC 3zzcC 3zzdC 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: 20429.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN COXSACKIEVIRUS / Strain: B3 / Plasmid: PET23A-COX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)GOLD References: UniProt: Q90092, UniProt: Q5UEA2*PLUS, picornain 3C |
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#2: Chemical | ChemComp-G85 / |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.84 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100 MM TRIS-HCL PH 8.5, 0.2 M MAGNESIUM CHLORIDE, AND 22% PEG 4000; SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→34.89 Å / Num. obs: 9954 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.28 / Net I/σ(I): 3.3 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CRYSTAL STRUCTURE OF COXSACKIEVIURS B3 3C PROTEASE Resolution: 2.1→46.94 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.889 / SU B: 6.305 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.275 / ESU R Free: 0.224 / 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: 21.149 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→46.94 Å
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