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Yorodumi- PDB-5w26: INFLUENZA VIRUS NEURAMINIDASE N9 IN COMPLEX WITH 4-DEOXYGENATED 2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w26 | |||||||||
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Title | INFLUENZA VIRUS NEURAMINIDASE N9 IN COMPLEX WITH 4-DEOXYGENATED 2,3-DIFLUORO-N-ACETYLNEURAMINIC ACID | |||||||||
Components | Neuraminidase | |||||||||
Keywords | hydrolase/hydrolase inhibitor / INFLUENZA VIRUS NEURAMINIDASE / N9 / COMPLEX / 4-DEOXYGENATED 2 / 3-DIFLUORO-N-ACETYLNEURAMINIC ACID / SECOND BINDING SITE / HYDROLASE / hydrolase-hydrolase inhibitor complex | |||||||||
Function / homology | Function and homology information : / : / : / 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: 1.9 Å | |||||||||
Authors | Streltsov, V.A. / Mckimm-Breschkin, J. / Barrett, S. / Pilling, P. / Hader, S. / Watt, A.G. | |||||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: Structural and Functional Analysis of Anti-Influenza Activity of 4-, 7-, 8- and 9-Deoxygenated 2,3-Difluoro- N-acetylneuraminic Acid Derivatives. Authors: McKimm-Breschkin, J.L. / Barrett, S. / Pilling, P.A. / Hader, S. / Watts, A.G. / Streltsov, V.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w26.cif.gz | 112.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w26.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 5w26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5w26_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 5w26_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 5w26_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 5w26_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/5w26 ftp://data.pdbj.org/pub/pdb/validation_reports/w2/5w26 | HTTPS FTP |
-Related structure data
Related structure data | 5w2uC 5w2wC 5w2yC 4wegS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43723.770 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 82-469 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9) Strain: A/Tern/Australia/G70C/1975 H11N9 / Gene: NA / Cell line (production host): HIGH FIVE / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03472, exo-alpha-sialidase |
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-Sugars , 5 types, 5 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Sugar | ChemComp-9SG / ( |
#5: Sugar | ChemComp-NAG / |
#8: Sugar | ChemComp-9VP / |
-Non-polymers , 3 types, 432 molecules
#6: Chemical | ChemComp-CA / |
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#7: Chemical | ChemComp-9WM / ( |
#9: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 1.7M POTASSIUM PHOSPHATE / PH range: 6.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9532 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 19, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9532 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.36 Å / Num. obs: 37832 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 72 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 39 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 25 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2735 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WEG Resolution: 1.9→42 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.746 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.107 / 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: 23.83 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→42 Å
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Refine LS restraints |
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