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Yorodumi- PDB-6hcx: Influenza Virus N9 Neuraminidase A complex with Zanamivir molecul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hcx | |||||||||
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Title | Influenza Virus N9 Neuraminidase A complex with Zanamivir molecule (Tern). | |||||||||
Components | Neuraminidase | |||||||||
Keywords | HYDROLASE / Complex / Zanamivir / Relenza / Neuraminidase / N9 / Influenza / Virus / Enzyme / Inhibitor | |||||||||
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: 1.3 Å | |||||||||
Authors | Salinger, M.T. / Hobbs, J.R. / Murray, J.W. / Laver, W.G. / Kuhn, P. / Garman, E.F. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: High Resolution Structures of Viral Neuraminidase with Drugs Bound in the Active Site. (In preparation) Authors: Salinger, M.T. / Hobbs, J.R. / Murray, J.W. / Laver, W.G. / Kuhn, P. / Garman, E.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hcx.cif.gz | 216 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hcx.ent.gz | 170.3 KB | Display | PDB format |
PDBx/mmJSON format | 6hcx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/6hcx ftp://data.pdbj.org/pub/pdb/validation_reports/hc/6hcx | HTTPS FTP |
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-Related structure data
Related structure data | 6hfcC 6hfyC 6hg0C 6hgbC 1f8eS 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9) Gene: NA / Production host: Gallus gallus (chicken) / References: UniProt: P03472, exo-alpha-sialidase |
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-Sugars , 3 types, 4 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)]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 | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-ZMR / | |
-Non-polymers , 4 types, 697 molecules
#4: Chemical | #5: Chemical | #7: Chemical | ChemComp-K / | #8: Water | ChemComp-HOH / | |
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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: 2.82 Å3/Da / Density % sol: 56.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: N9 crystals were grown by hanging-drop vapour diffusion against a reservoir of 1.9M potassium phosphate, pH 6.8, starting with equal volumes of N9 NA (10-15 mg/ml in water) and potassium ...Details: N9 crystals were grown by hanging-drop vapour diffusion against a reservoir of 1.9M potassium phosphate, pH 6.8, starting with equal volumes of N9 NA (10-15 mg/ml in water) and potassium phosphate buffer 1.4M KH2PO4:3M K2HPO4 in ratio 8:4, pH 6.6 at 20 degrees celsius. Inhibitor complexes obtained by soaking N9 crystals in a solution of 1.4M potassium phosphate buffer, pH 6.8, containing 5mM of inhibitor for 3 hours at 18 degrees celsius. Soaked in glycerol cryo-buffer. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→42.68 Å / Num. obs: 122689 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 12.3 Å2 / Rrim(I) all: 0.093 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.3→1.4 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 8993 / Rrim(I) all: 0.706 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F8E Resolution: 1.3→42.68 Å / Cor.coef. Fo:Fc: 0.989 / Cor.coef. Fo:Fc free: 0.984 / SU B: 1.153 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.031 / 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: 15.039 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→42.68 Å
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Refine LS restraints |
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