[English] 日本語
Yorodumi- PDB-1b9s: NOVEL AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE MAKE S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b9s | ||||||
---|---|---|---|---|---|---|---|
Title | NOVEL AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE MAKE SELECTIVE INTERACTIONS WITH CONSERVED RESIDUES AND WATER MOLECULES IN THE ACTIVE SITE | ||||||
Components | PROTEIN (NEURAMINIDASE) | ||||||
Keywords | HYDROLASE / NEURAMINIDASE / SIALIDASE / INFLUENZA | ||||||
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 B virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Finley, J.B. / Atigadda, V.R. / Duarte, F. / Zhao, J.J. / Brouillette, W.J. / Air, G.M. / Luo, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Novel aromatic inhibitors of influenza virus neuraminidase make selective interactions with conserved residues and water molecules in the active site. Authors: Finley, J.B. / Atigadda, V.R. / Duarte, F. / Zhao, J.J. / Brouillette, W.J. / Air, G.M. / Luo, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1b9s.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1b9s.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 1b9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/1b9s ftp://data.pdbj.org/pub/pdb/validation_reports/b9/1b9s | HTTPS FTP |
---|
-Related structure data
Related structure data | 1b9tC 1b9vC 1ivbS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 43460.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Influenza B virus (B/Lee/40) / Genus: Influenzavirus BInfluenza B virus / Cellular location: CELL MEMBRANE / Species: Influenza B virus / Strain: B/Lee/40 / References: UniProt: P03474, exo-alpha-sialidase | ||||
---|---|---|---|---|---|
#2: Sugar | ChemComp-NAG / | ||||
#3: Chemical | #4: Chemical | ChemComp-FDI / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.17 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.8 / Details: pH 6.8 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Sudbeck, E.A., (1997) J. Mol. Biol., 267, 584. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 295 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Aug 1, 1998 |
Radiation | Monochromator: GRAPHIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 17239 / % possible obs: 86.4 % / Observed criterion σ(I): 2 / Redundancy: 1.72 % / Rsym value: 0.124 / Net I/σ(I): 2.06 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 1.72 % / Mean I/σ(I) obs: 2.06 / Rsym value: 0.42 / % possible all: 86.44 |
Reflection | *PLUS Rmerge(I) obs: 0.124 |
Reflection shell | *PLUS % possible obs: 69.5 % / Rmerge(I) obs: 0.0042 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IVB Resolution: 2.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.85 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.174 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.345 / Rfactor obs: 0.252 |