[English] 日本語
![](img/lk-miru.gif)
- PDB-6v9e: The crystal structure of the 2009 H1N1 PA endonuclease wild type ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6v9e | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of the 2009 H1N1 PA endonuclease wild type in complex with SJ000988632 | ||||||
![]() | 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 58.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 39.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 13.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6v6xC ![]() 6vbrC ![]() 6vg9C ![]() 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 |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23148.344 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: ![]() ![]() |
---|
-Non-polymers , 5 types, 50 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/QQP.gif)
![](data/chem/img/Y24.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/QQP.gif)
![](data/chem/img/Y24.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-QQP / | #4: Chemical | ChemComp-Y24 / | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.01 % |
---|---|
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 |
---|---|
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: 2.4→64.38 Å / Num. obs: 11142 / % possible obs: 98.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 72.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.017 / Rrim(I) all: 0.038 / Χ2: 1.1 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1145 / CC1/2: 0.812 / Rpim(I) all: 0.403 / Rrim(I) all: 0.908 / Χ2: 1.04 / % possible all: 99.6 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5vpt Resolution: 2.4→38.96 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 39.84
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 164.96 Å2 / Biso mean: 83.2572 Å2 / Biso min: 41.66 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→38.96 Å
| |||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
|