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- PDB-1w1x: Structure of Neuraminidase from English duck subtype N6 complexed... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1w1x | |||||||||
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Title | Structure of Neuraminidase from English duck subtype N6 complexed with 30 mM sialic acid (NANA, Neu5Ac), crystal soaked for 3 hours at 277 K. | |||||||||
![]() | NEURAMINIDASE | |||||||||
![]() | HYDROLASE / INFLUENZA TYPE A / NEURAMINIDASE / HB SITE / SIALIC ACID / SUBTYPE N6 | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Rudino-Pinera, E. / Tunnah, P. / Crennell, S.J. / Webster, R.G. / Laver, W.G. / Garman, E.F. | |||||||||
![]() | ![]() Title: The Crystal Structure of Type a Influenza Virus Neuraminidase of the N6 Subtype Reveals the Existence of Two Separate Neu5Ac Binding Sites Authors: Rudino-Pinera, E. / Tunnah, P. / Crennell, S.J. / Webster, R.G. / Laver, W.G. / Garman, E.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 | ![]() | 362.5 KB | Display | ![]() |
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PDB format | ![]() | 288.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.9 MB | Display | ![]() |
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Full document | ![]() | 4.9 MB | Display | |
Data in XML | ![]() | 79.6 KB | Display | |
Data in CIF | ![]() | 114.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1w20C ![]() 1w21C ![]() 2cmlC ![]() 1v0zS 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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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 43011.531 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH SIALIC ACID / Source: (gene. exp.) ![]() ![]() Description: INFLUENZA VIRUS GROWN IN EMBRIONATED CHICKEN EGGS Production host: ![]() ![]() |
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-Sugars , 9 types, 25 molecules ![](data/chem/img/SIA.gif)
![](data/chem/img/MAN.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/BMA.gif)
![](data/chem/img/MAN.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/BMA.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose Source method: isolated from a genetically manipulated source | ||||||||||||||
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 #5: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose / 6alpha-alpha-mannobiose | #6: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-SIA / #9: Sugar | ChemComp-MAN / #10: Sugar | ChemComp-NAG / #13: Sugar | ChemComp-BMA / | |
-Non-polymers , 4 types, 1574 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#8: Chemical | ChemComp-CA / #11: Chemical | ChemComp-GOL / #12: Chemical | ChemComp-PEG / | #14: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.86 % |
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Crystal grow | Temperature: 293 K / pH: 7 / Details: 0.15 M NACL, 20% PEG 3350 AT 293 K, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 15, 2004 / Details: 1.2 METRE LONG SILICON SUBSTRATE, RHODIUM COATED |
Radiation | Monochromator: SILICON 11 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9853 Å / Relative weight: 1 |
Reflection | Resolution: 2→33.78 Å / Num. obs: 112032 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 16.63 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.3 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1V0Z Resolution: 2→33.71 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.684 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: UNLIKE OTHER VIRAL NEURAMINIDASES SOLVED TO DATE, N6 HAS A FULL TETRAMER IN THE ASYMMETRIC UNIT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2→33.71 Å
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Refine LS restraints |
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