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- PDB-5wf3: Crystal structure of the influenza virus PA endonuclease (E119D m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5wf3 | ||||||||||||
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Title | Crystal structure of the influenza virus PA endonuclease (E119D mutant) in complex with inhibitor 9k (SRI-30023) | ||||||||||||
![]() | 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 | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.1 KB | Display | ![]() |
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PDB format | ![]() | 68.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5w3iC ![]() 5w44C ![]() 5w73C ![]() 5w7uC ![]() 5w92C ![]() 5w9gC ![]() 5wa6C ![]() 5wa7C ![]() 5wapC ![]() 5wb3C ![]() 5wcsC ![]() 5wctC ![]() 5wdcC ![]() 5wdnC ![]() 5wdwC ![]() 5we9C ![]() 5webC ![]() 5wefC ![]() 5weiC ![]() 5wfmC ![]() 5wfwC ![]() 5wfzC ![]() 5wg9C 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: 23134.316 Da / Num. of mol.: 1 Mutation: E119D, Loop 51-72 is replaced by a GGS linker, N-terminal has His-tag residues Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-KU2 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.4 Details: 1 M Ammonium sulfate, 0.1 M CAPSO pH 9.4, 50 mM MnCl2, 50 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 20, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 13414 / % possible obs: 98.6 % / Redundancy: 9.5 % / Biso Wilson estimate: 51.21 Å2 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.042 / Rrim(I) all: 0.136 / Χ2: 1.55 / Net I/σ(I): 9.5 / Num. measured all: 127674 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 149.09 Å2 / Biso mean: 73.4604 Å2 / Biso min: 42 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.251→32.06 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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Refinement TLS params. | Method: refined / Origin x: 128.7092 Å / Origin y: 202.4605 Å / Origin z: 285.5328 Å
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Refinement TLS group |
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