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- PDB-6vg9: The crystal structure of the 2009 H1N1/California PA endonuclease... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vg9 | ||||||
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Title | The crystal structure of the 2009 H1N1/California PA endonuclease I38T mutant in complex with SJ000986248 | ||||||
![]() | Polymerase acidic protein | ||||||
![]() | VIRAL PROTEIN / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE / HYDROLASE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cuypers, M.G. / Slavish, P.J. / Rankovic, Z. / White, S.W. | ||||||
![]() | ![]() Title: Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential. Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / ...Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / Min, J. / Webby, R.J. / Rankovic, Z. / White, S.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.6 KB | Display | ![]() |
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PDB format | ![]() | 37.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 12.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6v6xC ![]() 6v9eC ![]() 6vbrC ![]() 6vivC ![]() 6vjhC ![]() 6vl3C ![]() 6wijC ![]() 6wj4C ![]() 7k87C ![]() 7lm4C ![]() 7lw6C ![]() 7m0nC ![]() 7mpfC ![]() 7mtyC ![]() 7n47C ![]() 7n55C ![]() 7n68C ![]() 7n8fC ![]() 7rkpC ![]() 7umrC ![]() 7uuhC ![]() 8dipC ![]() 8dpjC ![]() 8dtwC ![]() 8e4sC ![]() 5vptS C: citing same article ( S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23136.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/Luxembourg/43/2009(H1N1) / Gene: PA / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 26 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/QQ4.gif)
![](data/chem/img/QVV.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/QQ4.gif)
![](data/chem/img/QVV.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-QQ4 / | #4: Chemical | ChemComp-QVV / | #5: Chemical | ChemComp-SO4 / | #6: 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: 3.26 Å3/Da / Density % sol: 62.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES PH 7.8, 1 M AMMONIUM SULFATE, 10 MM MNCL2, 10 MM MGCL2, 0.5% PVP K15 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→75.01 Å / Num. obs: 7509 / % possible obs: 99.4 % / Redundancy: 5.3 % / Biso Wilson estimate: 71.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.029 / Rrim(I) all: 0.067 / Χ2: 1.04 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.75→2.88 Å / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 992 / CC1/2: 0.726 / Rpim(I) all: 0.43 / Χ2: 1.04 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5vpt Resolution: 2.75→40.02 Å / SU ML: 0.7 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.95
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 143.04 Å2 / Biso mean: 83.4278 Å2 / Biso min: 44.6 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.75→40.02 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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