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Yorodumi- PDB-4hzx: Crystal structure of influenza A neuraminidase N3 complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hzx | |||||||||
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Title | Crystal structure of influenza A neuraminidase N3 complexed with oseltamivir | |||||||||
Components | Neuraminidase | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / neuraminidase / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
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: 2.2 Å | |||||||||
Authors | Li, Q. / Qi, J. / Vavricka, C.J. / Gao, G.F. | |||||||||
Citation | Journal: J.Virol. / Year: 2013 Title: Functional and structural analysis of influenza virus neuraminidase N3 offers further insight into the mechanisms of oseltamivir resistance. Authors: Li, Q. / Qi, J. / Wu, Y. / Kiyota, H. / Tanaka, K. / Suhara, Y. / Ohrui, H. / Suzuki, Y. / Vavricka, C.J. / Gao, G.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hzx.cif.gz | 169.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hzx.ent.gz | 131.1 KB | Display | PDB format |
PDBx/mmJSON format | 4hzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/4hzx ftp://data.pdbj.org/pub/pdb/validation_reports/hz/4hzx | HTTPS FTP |
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-Related structure data
Related structure data | 4hzvC 4hzwC 4hzyC 4hzzC 4i00C 2batS C: citing same article (ref.) S: Starting model for refinement |
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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: 43327.680 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 83-469 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: NA / Cell (production host): Hi5 / References: UniProt: A9YN63 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 343 molecules
#4: Chemical | #5: Chemical | ChemComp-G39 / ( | #6: 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: 2.16 Å3/Da / Density % sol: 43.14 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 8 Details: 20mM Tris, pH 8.0, 50mM NaCl, 0.1M BIS-TRIS propane (pH 9.0), 10% v/v Jeffamine ED-2001 (pH 7.0) , VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 20, 2010 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 17390 / Num. obs: 17390 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BAT Resolution: 2.2→38.645 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 18.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.067 Å2 / ksol: 0.351 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→38.645 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: 6
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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