[English] 日本語
![](img/lk-miru.gif)
- PDB-8djv: The N-terminal domain of PA endonuclease from the influenza H1N1 ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8djv | ||||||
---|---|---|---|---|---|---|---|
Title | The N-terminal domain of PA endonuclease from the influenza H1N1 viral polymerase in complex with 6-Bromo-3-hydroxy-N-methoxy-4-oxo-1,4-dihydropyridine-2-carboxamide | ||||||
![]() | Polymerase acidic protein | ||||||
![]() | VIRAL PROTEIN / HYDROLASE/INHIBITOR / Drug discovery / metal-binding pharmacophore / isosteres / influenza endonuclease / VIRAL PROTEIN-INHIBITOR complex / ANTIVIRAL PROTEIN / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / viral RNA genome replication / RNA binding / : / Chem-U3U / Protein PA-X![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kohlbrand, A.J. / Stokes, R.W. / Karges, J. / Seo, H. / Sankaran, B. / Cohen, S.M. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Carboxylic Acid Isostere Derivatives of Hydroxypyridinones as Core Scaffolds for Influenza Endonuclease Inhibitors. Authors: Stokes, R.W. / Kohlbrand, A.J. / Seo, H. / Sankaran, B. / Karges, J. / Cohen, S.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 105.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 69.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7v04C ![]() 8ctfC ![]() 8dalC ![]() 8ddbC ![]() 8ddeC ![]() 8dhnC ![]() 8djyC ![]() 6e6vS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 22424.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-U3U / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.5 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 32% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: APEX II CCD / Detector: CCD / Date: Aug 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→37.24 Å / Num. obs: 22176 / % possible obs: 99.1 % / Redundancy: 17.7 % / Biso Wilson estimate: 37.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.023 / Rrim(I) all: 0.103 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.08→2.15 Å / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1077 / CC1/2: 0.723 / Rrim(I) all: 0.815 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6E6V Resolution: 2.08→37.23 Å / SU ML: 0.3637 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.8966 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→37.23 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
|