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- PDB-4e5h: Crystal structure of avian influenza virus PAn bound to compound 3 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4e5h | ||||||
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Title | Crystal structure of avian influenza virus PAn bound to compound 3 | ||||||
![]() | Polymerase protein PA | ||||||
![]() | VIRAL PROTEIN / TRANSCRIPTION / endonuclease domain / H5N1 subtype | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | DuBois, R.M. / Slavish, P.J. / Webb, T.R. / White, S.W. | ||||||
![]() | ![]() Title: Structural and Biochemical Basis for Development of Influenza Virus Inhibitors Targeting the PA Endonuclease. Authors: Dubois, R.M. / Slavish, P.J. / Baughman, B.M. / Yun, M.K. / Bao, J. / Webby, R.J. / Webb, T.R. / White, S.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.5 KB | Display | ![]() |
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PDB format | ![]() | 126.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4e5eSC ![]() 4e5fC ![]() 4e5gC ![]() 4e5iC ![]() 4e5jC ![]() 4e5lC 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21915.959 Da / Num. of mol.: 4 / Fragment: SEE REMARK 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-0N8 / ( | #5: Water | ChemComp-HOH / | Sequence details | PROTEIN COMPRISES UNP RESIDUES 1-50 AND 73-196 SEPARATED BY A GLY-GLY-SER LINKER. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.5 M ammonium sulfate, 2% PEG1500, 1 mM manganese chloride, 0.1 M Tris-Cl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.158→46.048 Å / Num. all: 57783 / Num. obs: 57667 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.087 / Net I/σ(I): 15.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4E5E Resolution: 2.158→46.048 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.901 / WRfactor Rfree: 0.3152 / WRfactor Rwork: 0.2746 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7685 / SU B: 0.002 / SU ML: 0 / SU R Cruickshank DPI: 0.2463 / SU Rfree: 0.2086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: ELECTRON DENSITY AT THE ACTIVE SITES OF CHAINS A, B, AND C SUGGESTS THE PRESENCE OF LIGAND 0N8 (COMPOUND 3), BUT IS INSUFFICIENT TO MODEL THE LIGAND.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.34 Å2 / Biso mean: 47.7666 Å2 / Biso min: 27.78 Å2
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Refinement step | Cycle: LAST / Resolution: 2.158→46.048 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.158→2.213 Å / Total num. of bins used: 20
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