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Yorodumi- PDB-4ks2: Influenza Neuraminidase in complex with antiviral compound (3S,4R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ks2 | ||||||
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Title | Influenza Neuraminidase in complex with antiviral compound (3S,4R,5R)-4-(acetylamino)-3-carbamimidamido-5-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid | ||||||
Components | Neuraminidase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Sialidase / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.595 Å | ||||||
Authors | Kerry, P.S. / Russell, R.J.M. | ||||||
Citation | Journal: Sci Rep / Year: 2013 Title: Structural basis for a class of nanomolar influenza A neuraminidase inhibitors. Authors: Kerry, P.S. / Mohan, S. / Russell, R.J.M. / Bance, N. / Niikura, M. / Pinto, B.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ks2.cif.gz | 95.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ks2.ent.gz | 70 KB | Display | PDB format |
PDBx/mmJSON format | 4ks2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/4ks2 ftp://data.pdbj.org/pub/pdb/validation_reports/ks/4ks2 | HTTPS FTP |
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-Related structure data
Related structure data | 4ks1C 4ks3C 4ks4C 4ks5C 2ht5S 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
#1: Protein | Mass: 43196.664 Da / Num. of mol.: 1 / Fragment: UNP residues 81-470 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Duck/Ukraine/1/1963 H3N8 / Gene: NA / Production host: Escherichia coli (E. coli) / References: UniProt: Q0A480 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-1SJ / ( |
#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: 2.18 Å3/Da / Density % sol: 43.67 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 40% 2-methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 17, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: -h,k,-l / Fraction: 0.77 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.59→30 Å / Num. all: 11553 / Num. obs: 10242 / % possible obs: 88.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 10.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HT5 Resolution: 2.595→23.435 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 1.35 / Phase error: 20.43 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.372 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.595→23.435 Å
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Refine LS restraints |
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LS refinement shell |
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