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Open data
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Basic information
Entry | Database: PDB / ID: 6ku8 | ||||||
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Title | structure of HRV-C 3C protein with rupintrivir | ||||||
![]() | Genome polyprotein | ||||||
![]() | HYDROLASE / HRV / 3C / protease / rupintrivir | ||||||
Function / homology | ![]() 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 / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell 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 / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhu, L. / Yuan, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the HRV-C 3C-Rupintrivir Complex Provides New Insights for Inhibitor Design. Authors: Yuan, S. / Fan, K. / Chen, Z. / Sun, Y. / Hou, H. / Zhu, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56 KB | Display | ![]() |
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PDB format | ![]() | 37.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 880.2 KB | Display | ![]() |
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Full document | ![]() | 883.7 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ku7C ![]() 3zv8S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 20608.455 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: E5D8F2, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
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#2: Chemical | ChemComp-AG7 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.08 % |
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Crystal grow | Temperature: 289.15 K / Method: batch mode Details: 0.05 M citric acid, 0.05 M BIS-TRIS propane, pH 5.0, 16% (w/v) polyethylene glycol 3,350. |
-Data collection
Diffraction | Mean temperature: 293.15 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.998 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 16114 / % possible obs: 92.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 0.263 / Num. unique obs: 1496 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ZV8 Resolution: 2.05→50 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.05→50 Å
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LS refinement shell | Resolution: 2.05→2.21 Å / Rfactor Rfree: 0.233 / Rfactor Rwork: 0.1859 |