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Yorodumi- PDB-5nzf: Complex of H275Y/I223V mutant variant of neuraminidase from H1N1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nzf | |||||||||
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Title | Complex of H275Y/I223V mutant variant of neuraminidase from H1N1 influenza virus with oseltamivir | |||||||||
Components | Neuraminidase | |||||||||
Keywords | VIRAL PROTEIN / neuraminidase / influenza / complex / 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 | unidentified influenza virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å | |||||||||
Authors | Pachl, P. / Pokorna, J. | |||||||||
Citation | Journal: Viruses / Year: 2018 Title: Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Authors: Pokorna, J. / Pachl, P. / Karlukova, E. / Hejdanek, J. / Rezacova, P. / Machara, A. / Hudlicky, J. / Konvalinka, J. / Kozisek, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nzf.cif.gz | 344.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nzf.ent.gz | 276.3 KB | Display | PDB format |
PDBx/mmJSON format | 5nzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/5nzf ftp://data.pdbj.org/pub/pdb/validation_reports/nz/5nzf | HTTPS FTP |
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-Related structure data
Related structure data | 5nweSC 5nz4C 5nzeC 5nznC 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 42738.629 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified influenza virus / Gene: NA / Production host: Escherichia coli (E. coli) / References: UniProt: W5R8B8, UniProt: C3W6G3*PLUS |
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-Sugars , 3 types, 11 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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 |
#6: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 1350 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-G39 / ( #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-NA / | #9: 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: 3.08 Å3/Da / Density % sol: 60.07 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M HEPES pH 7.0, 7% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.745→45.18 Å / Num. obs: 207846 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.36 % / Biso Wilson estimate: 23.93 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.114 / Net I/σ(I): 8.97 |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 3.23 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 32725 / CC1/2: 0.71 / Rrim(I) all: 0.673 / % possible all: 96.9 |
-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.566
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NWE Resolution: 1.75→45.18 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.911 / SU B: 3.014 / SU ML: 0.094 / SU R Cruickshank DPI: 0.1132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.116 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 61.32 Å2 / Biso mean: 18.781 Å2 / Biso min: 7.71 Å2
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Refinement step | Cycle: final / Resolution: 1.75→45.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.745→1.791 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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