+Open data
-Basic information
Entry | Database: PDB / ID: 3ckz | ||||||
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Title | N1 Neuraminidase H274Y + Zanamivir | ||||||
Components | Neuraminidase | ||||||
Keywords | VIRAL PROTEIN / HYDROLASE / N1 / Neuraminidase / H274Y / Zanamivir / Glycosidase / Membrane / Transmembrane / Virion | ||||||
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 / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Colllins, P. / Haire, L.F. / Lin, Y.P. / Liu, J. / Russell, R.J. / Walker, P.A. / Skehel, J.J. / Martin, S.R. / Hay, A.J. / Gamblin, S.J. | ||||||
Citation | Journal: Nature / Year: 2008 Title: Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants. Authors: Collins, P.J. / Haire, L.F. / Lin, Y.P. / Liu, J. / Russell, R.J. / Walker, P.A. / Skehel, J.J. / Martin, S.R. / Hay, A.J. / Gamblin, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ckz.cif.gz | 87.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ckz.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ckz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/3ckz ftp://data.pdbj.org/pub/pdb/validation_reports/ck/3ckz | 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
#1: Protein | Mass: 42209.941 Da / Num. of mol.: 1 / Fragment: UNP residues 63-447 / Mutation: H274Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: NA / Production host: Influenza A virus / Strain (production host): WSN-NA (H1N1) / References: UniProt: Q6DPL2, exo-alpha-sialidase |
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#2: Chemical | ChemComp-CA / |
#3: Sugar | ChemComp-ZMR / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 15% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 3, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 30055 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.9→2 Å / % possible all: 61.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.34 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: RESIDUE (A ASN 306 ) AND RESIDUE (A GLN 308 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 2.04. RESIDUE (A GLY 333 ) AND RESIDUE (A SER 335 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 1.85. ...Details: RESIDUE (A ASN 306 ) AND RESIDUE (A GLN 308 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 2.04. RESIDUE (A GLY 333 ) AND RESIDUE (A SER 335 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 1.85. RESIDUE (A CYS 336 ) AND RESIDUE (A GLY 339 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 1.97. RESIDUE (A SER 342 ) AND RESIDUE (A SER 344 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 2.07. RESIDUE (A VAL 392 ) AND RESIDUE (A LYS 394 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 1.76. RESIDUE (A GLU 433 ) AND RESIDUE (A SER 435 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 1.87.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.683 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.902→1.951 Å / Total num. of bins used: 20
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