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- PDB-3ti6: Crystal structure of 2009 pandemic H1N1 neuraminidase complexed w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ti6 | |||||||||
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Title | Crystal structure of 2009 pandemic H1N1 neuraminidase complexed with oseltamivir | |||||||||
![]() | Neuraminidase![]() | |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / 6-BLADED BETA-PROPELLER / ![]() ![]() ![]() | |||||||||
Function / homology | ![]() exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Vavricka, C.J. / Li, Q. / Wu, Y. / Qi, J. / Wang, M. / Liu, Y. / Gao, F. / Liu, J. / Feng, E. / He, J. ...Vavricka, C.J. / Li, Q. / Wu, Y. / Qi, J. / Wang, M. / Liu, Y. / Gao, F. / Liu, J. / Feng, E. / He, J. / Wang, J. / Liu, H. / Jiang, H. / Gao, G.F. | |||||||||
![]() | ![]() Title: Structural and functional analysis of laninamivir and its octanoate prodrug reveals group specific mechanisms for influenza NA inhibition Authors: Vavricka, C.J. / Li, Q. / Wu, Y. / Qi, J. / Wang, M. / Liu, Y. / Gao, F. / Liu, J. / Feng, E. / He, J. / Wang, J. / Liu, H. / Jiang, H. / Gao, G.F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 349.7 KB | Display | ![]() |
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PDB format | ![]() | 282.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ti3C ![]() 3ti4C ![]() 3ti5C ![]() 3ti8C ![]() 3tiaC ![]() 3tibC ![]() 3ticC ![]() 3nssS 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | ![]() Mass: 42727.629 Da / Num. of mol.: 2 / Fragment: UNP residues 82-469 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Sugars , 2 types, 5 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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: Sugar | ChemComp-NAG / ![]() |
-Non-polymers , 5 types, 817 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/G39.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/G39.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / #5: Chemical | ![]() #6: Chemical | ![]() #7: Chemical | ChemComp-ACT / ![]() #8: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.3 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.16M calcium acetate hydrate, 0.08M sodium cacodylate trihydrate, 14.4% polyethylene glycol 8000, 20% glycerol , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2010 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.69→50 Å / Num. all: 107418 / Num. obs: 107418 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 8.64 Å2 |
Reflection shell | Resolution: 1.69→1.76 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3NSS Resolution: 1.69→28.998 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.9125 / SU ML: 0.17 / σ(F): 0.1 / Phase error: 15.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.824 Å2 / ksol: 0.368 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.32 Å2 / Biso mean: 12.3498 Å2 / Biso min: 2.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→28.998 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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