[English] 日本語
Yorodumi- PDB-6e6w: The N-terminal domain of PA endonuclease from the influenza H1N1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6e6w | ||||||
---|---|---|---|---|---|---|---|
Title | The N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 3-hydroxy-6-(2-methyl-4-(1H-tetrazol-5-yl)phenyl)-4-oxo-1,4-dihydropyridine-2-carboxylic acid | ||||||
Components | Polymerase acidic protein | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / PA endonuclease / inhibitor / influenza / H1N1 / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Dick, B.L. / Morrison, C.N. / Credille, C.V. / Cohen, S.M. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: J.Med.Chem. / Year: 2019 Title: SAR Exploration of Tight-Binding Inhibitors of Influenza Virus PA Endonuclease. Authors: Credille, C.V. / Morrison, C.N. / Stokes, R.W. / Dick, B.L. / Feng, Y. / Sun, J. / Chen, Y. / Cohen, S.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6e6w.cif.gz | 54.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6e6w.ent.gz | 36.5 KB | Display | PDB format |
PDBx/mmJSON format | 6e6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e6w_validation.pdf.gz | 724 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6e6w_full_validation.pdf.gz | 725.1 KB | Display | |
Data in XML | 6e6w_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 6e6w_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/6e6w ftp://data.pdbj.org/pub/pdb/validation_reports/e6/6e6w | HTTPS FTP |
-Related structure data
Related structure data | 6e3mC 6e3nC 6e3oC 6e3pC 6e4cC 6e6vC 6e6xC 4awmS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22468.666 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: swl A/California/04/2009 H1N1 / Gene: PA / Production host: Escherichia coli BL21 (bacteria) References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-HWJ / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.15 % |
---|---|
Crystal grow | Temperature: 306 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 30% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2017 |
Radiation | Monochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→44.05 Å / Num. obs: 8854 / % possible obs: 100 % / Redundancy: 31.4 % / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.022 / Rrim(I) all: 0.092 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 31.1 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 7.3 / Num. unique obs: 831 / Rpim(I) all: 0.107 / Rrim(I) all: 0.439 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4AWM Resolution: 2.35→44.05 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.542 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.406 / ESU R Free: 0.277 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.986 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.35→44.05 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|