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- PDB-6dcy: The N-terminal domain of PA endonuclease from the influenza H1N1 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dcy | ||||||
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Title | The N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 5-hydroxy-2-methyl-4-oxo-4H-pyran-3-carboxylic acid | ||||||
![]() | Polymerase acidic protein | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Inhibitor / Endonuclease / Influenza / PA domain / 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 | ![]() ![]() ![]() | ||||||
![]() | Dick, B.L. / Morrison, C.N. / Cohen, S.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Activity Relationships in Metal-Binding Pharmacophores for Influenza Endonuclease. Authors: Credille, C.V. / Dick, B.L. / Morrison, C.N. / Stokes, R.W. / Adamek, R.N. / Wu, N.C. / Wilson, I.A. / Cohen, S.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.5 KB | Display | ![]() |
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PDB format | ![]() | 36.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 764.5 KB | Display | ![]() |
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Full document | ![]() | 766.1 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dczC ![]() 6dzqC ![]() 6e0qC ![]() 4awmS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22468.666 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-198) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds | ||||
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#2: Chemical | #3: Chemical | ChemComp-G5V / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.24 % / Description: Octahedron |
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Crystal grow | Temperature: 306 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.5 mM inhibitor, 25-40% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 2.08→37.77 Å / Num. obs: 12849 / % possible obs: 100 % / Redundancy: 16.9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.08→2.14 Å / Redundancy: 18.1 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 974 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4AWM Resolution: 2.08→37.77 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.26 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.203 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.595 Å2
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Refinement step | Cycle: 1 / Resolution: 2.08→37.77 Å
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Refine LS restraints |
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