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- PDB-7nug: Influenza A/California/07/2009(H1N1) endonuclease in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7nug | |||||||||
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Title | Influenza A/California/07/2009(H1N1) endonuclease in complex with orientin | |||||||||
![]() | Polymerase acidic protein,Polymerase acidic protein | |||||||||
![]() | VIRAL PROTEIN / endonuclease / protein-ligand complex / RNA polymerase / Flavonoids | |||||||||
Function / homology | ![]() cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Radilova, K. / Brynda, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Synthesis and In Vitro Evaluation of C-7 and C-8 Luteolin Derivatives as Influenza Endonuclease Inhibitors. Authors: Reiberger, R. / Radilova, K. / Kral, M. / Zima, V. / Majer, P. / Brynda, J. / Dracinsky, M. / Konvalinka, J. / Kozisek, M. / Machara, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.8 KB | Display | ![]() |
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PDB format | ![]() | 43.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.9 KB | Display | ![]() |
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Full document | ![]() | 439.2 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 17.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nuhC ![]() 6ya5S 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 21208.182 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/California/07/2009(H1N1) / Gene: PA / Production host: ![]() ![]() References: UniProt: C3W5X6, Hydrolases; Acting on ester bonds |
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-Non-polymers , 8 types, 202 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/1PG.gif)
![](data/chem/img/USE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/1PG.gif)
![](data/chem/img/USE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | #5: Chemical | ChemComp-PG4 / | #6: Chemical | #7: Chemical | ChemComp-1PG / | #8: Chemical | ChemComp-USE / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.17 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MDP, PEG 1000, PEG 3350, Sodium HEPES, MOPS (acid), Magnesium chloride, Calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Aug 25, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→42.15 Å / Num. obs: 16879 / % possible obs: 99.5 % / Redundancy: 9.31 % / Biso Wilson estimate: 29.266 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.094 / Χ2: 0.907 / Net I/σ(I): 15.29 / Num. measured all: 157145 / Scaling rejects: 109 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6YA5 Resolution: 1.9→42.15 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2257 / WRfactor Rwork: 0.1701 / FOM work R set: 0.8082 / SU B: 4.517 / SU ML: 0.126 / SU R Cruickshank DPI: 0.1731 / SU Rfree: 0.1628 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.27 Å2 / Biso mean: 26.456 Å2 / Biso min: 11.65 Å2
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Refinement step | Cycle: final / Resolution: 1.9→42.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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