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Yorodumi- PDB-1f8d: Native Influenza Neuraminidase in Complex with 9-amino-2-deoxy-2,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f8d | |||||||||
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Title | Native Influenza Neuraminidase in Complex with 9-amino-2-deoxy-2,3-dehydro-N-neuraminic Acid | |||||||||
Components | NEURAMINIDASE | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / neuraminidase / hydrolase / influenza protein / glycosylated protein / 9-amino-DANA / 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 / Resolution: 1.4 Å | |||||||||
Authors | Smith, B.J. / Colman, P.M. / Von Itzstein, M. / Danylec, B. / Varghese, J.N. | |||||||||
Citation | Journal: Protein Sci. / Year: 2001 Title: Analysis of inhibitor binding in influenza virus neuraminidase. Authors: Smith, B.J. / Colman, P.M. / Von Itzstein, M. / Danylec, B. / Varghese, J.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f8d.cif.gz | 98.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f8d.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 1f8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/1f8d ftp://data.pdbj.org/pub/pdb/validation_reports/f8/1f8d | HTTPS FTP |
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-Related 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 Fragment: INTEGRAL MEMBRANE PROTEIN, MEMBRANE STALK CLEAVED BY PRONASE RELEASING FULLY ACTIVE RESIDUES 82-468 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/tern/Australia/G70C/1975(H11N9)) Genus: Influenzavirus A / Species: Influenza A virus / Strain: A/TERN/AUSTRALIA/G70C/75 / Genus (production host): Influenzavirus A / Production host: Influenza A virus / Strain (production host): RECOMBINANT (NWS/G70C) N9 References: GenBank: 324880, UniProt: P03472*PLUS, exo-alpha-sialidase |
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-Sugars , 4 types, 4 molecules A
#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-(1-6)]alpha-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 |
#4: Sugar | ChemComp-NAG / |
#6: Sugar |
-Non-polymers , 2 types, 365 molecules
#5: Chemical | #7: 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: 2.81 Å3/Da / Density % sol: 56.26 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: phosphate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / Details: Laver, W.G., (1984) Virology, 137, 314. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 17, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→60 Å / Num. all: 97900 / Num. obs: 72942 / % possible obs: 74.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.4→1.44 Å / Num. unique all: 4348 |
Reflection | *PLUS Num. measured all: 222071 |
Reflection shell | *PLUS % possible obs: 95.7 % |
-Processing
Software |
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Refinement | Resolution: 1.4→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_plane_restr / Dev ideal: 0.83 |