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Yorodumi- PDB-7e6q: Crystal structure of influenza A virus neuraminidase N5 complexed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7e6q | ||||||
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Title | Crystal structure of influenza A virus neuraminidase N5 complexed with 4'-phenyl-1,2,3-triazolylated oseltamivir carboxylate | ||||||
Components | Neuraminidase | ||||||
Keywords | HYDROLASE / Influenza virus / Neuraminidase inhibitors / Oseltamivir derivatives / 150-cavity | ||||||
Function / homology | Function and homology information exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wang, P.F. / Babayemi, O.O. / Li, C.N. / Fu, L.F. / Zhang, S.S. / Qi, J.X. / Lv, X. / Li, X.B. | ||||||
Funding support | 1items
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Citation | Journal: Rsc Adv / Year: 2021 Title: Structure-based design of 5'-substituted 1,2,3-triazolylated oseltamivir derivatives as potent influenza neuraminidase inhibitors. Authors: Wang, P. / Oladejo, B.O. / Li, C. / Fu, L. / Zhang, S. / Qi, J. / Lv, X. / Li, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e6q.cif.gz | 355.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e6q.ent.gz | 257 KB | Display | PDB format |
PDBx/mmJSON format | 7e6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e6q_validation.pdf.gz | 1018.7 KB | Display | wwPDB validaton report |
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Full document | 7e6q_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7e6q_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 7e6q_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/7e6q ftp://data.pdbj.org/pub/pdb/validation_reports/e6/7e6q | HTTPS FTP |
-Related structure data
Related structure data | 3sanS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43531.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Duck/Alberta/60/1976 H12N5) Strain: A/Duck/Alberta/60/1976 H12N5 / Gene: NA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A1ILL9, exo-alpha-sialidase #2: Chemical | #3: Sugar | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES (pH 7.5), 12% w/v Polyethylene glycol 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97919 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 42631 / % possible obs: 95.6 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.235 / Num. unique obs: 40762 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SAN Resolution: 2.2→32.37 Å / SU ML: 0.2138 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 34.0087 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→32.37 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 82 - 982 / Label seq-ID: 1
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