[English] 日本語
![](img/lk-miru.gif)
- PDB-5wa6: Crystal structure of the influenza virus PA endonuclease in compl... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5wa6 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the influenza virus PA endonuclease in complex with an inhibitor - SRI-30007 | ||||||||||||
![]() | Polymerase acidic protein | ||||||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Virus / Nuclease / Transcription / Cap-snatching / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||
![]() | Kumar, G. / White, S.W. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Protein-Structure Assisted Optimization of 4,5-Dihydroxypyrimidine-6-Carboxamide Inhibitors of Influenza Virus Endonuclease. Authors: Beylkin, D. / Kumar, G. / Zhou, W. / Park, J. / Jeevan, T. / Lagisetti, C. / Harfoot, R. / Webby, R.J. / White, S.W. / Webb, T.R. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 91.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 68.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5w3iC ![]() 5w44C ![]() 5w73C ![]() 5w7uC ![]() 5w92C ![]() 5w9gC ![]() 5wa7C ![]() 5wapC ![]() 5wb3C ![]() 5wcsC ![]() 5wctC ![]() 5wdcC ![]() 5wdnC ![]() 5wdwC ![]() 5we9C ![]() 5webC ![]() 5wefC ![]() 5weiC ![]() 5wf3C ![]() 5wfmC ![]() 5wfwC ![]() 5wfzC ![]() 5wg9C C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 23148.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-KU7 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.91 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 0.1 M HEPES pH 7.8, 1.0 M AmSO4, 10 mM MnCl2, 10 mM MgCl2, 1% PVP K15 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→50 Å / Num. obs: 13745 / % possible obs: 99.9 % / Redundancy: 7.8 % / Biso Wilson estimate: 57.79 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.025 / Rrim(I) all: 0.071 / Χ2: 1.281 / Net I/σ(I): 11.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 169.71 Å2 / Biso mean: 91.5786 Å2 / Biso min: 53.87 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→38.797 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 490.908 Å / Origin y: 202.292 Å / Origin z: 558.793 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|