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- PDB-5w2y: INFLUENZA VIRUS NEURAMINIDASE N9 IN COMPLEX WITH 9-DEOXYGENATED 2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5w2y | |||||||||
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Title | INFLUENZA VIRUS NEURAMINIDASE N9 IN COMPLEX WITH 9-DEOXYGENATED 2,3-DIFLUORO-N-ACETYLNEURAMINIC ACID | |||||||||
![]() | Neuraminidase | |||||||||
![]() | hydrolase/hydrolase inhibitor / INFLUENZA VIRUS NEURAMINIDASE / N9 / COMPLEX / 2 / 3-DIFLUOROSIALIC ACID / SECOND BINDING SITE / HYDROLASE / hydrolase-hydrolase inhibitor complex | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Streltsov, V.A. / Mckimm-Breschkin, J. / Barrett, S. / Pilling, P. / Hader, S. / Watt, A.G. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.4 KB | Display | ![]() |
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PDB format | ![]() | 82 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 22.6 KB | Display | |
Data in CIF | ![]() | 33.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w26C ![]() 5w2uC ![]() 5w2wC ![]() 4wegS C: citing same article ( S: Starting model for refinement |
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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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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.) ![]() Strain: A/Tern/Australia/G70C/1975 H11N9 / Gene: NA / Cell line (production host): HIGH FIVE / Production host: ![]() |
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-Sugars , 5 types, 5 molecules ![](data/chem/img/9T7.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/9T1.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/9T1.gif)
#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)]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-9T7 / ( |
#5: Sugar | ChemComp-NAG / |
#8: Sugar | ChemComp-9T1 / |
-Non-polymers , 3 types, 354 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/9TM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/9TM.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-CA / |
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#7: Chemical | ChemComp-9TM / ( |
#9: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953733 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→48.48 Å / Num. obs: 19147 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 35.4 % / Rmerge(I) obs: 0.394 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.39→2.45 Å / Redundancy: 16.6 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4WEG Resolution: 2.39→48.48 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.739 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.212 / 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: 22.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→48.48 Å
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Refine LS restraints |
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