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Yorodumi- PDB-1vcj: Influenza B virus neuraminidase complexed with 1-(4-Carboxy-2-(3-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vcj | |||||||||
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Title | Influenza B virus neuraminidase complexed with 1-(4-Carboxy-2-(3-pentylamino)phenyl)-5-aminomethyl-5-hydroxymethyl-pyrrolidin-2-one | |||||||||
Components | NEURAMINIDASE | |||||||||
Keywords | HYDROLASE / neuraminidase / benzoic acid inhibitors / small molecule inhibitor / protein-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 B virus | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Lommer, B.S. / Ali, S.M. / Bajpai, S.N. / Brouillette, W.J. / Air, G.M. / Luo, M. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: A benzoic acid inhibitor induces a novel conformational change in the active site of Influenza B virus neuraminidase. Authors: Lommer, B.S. / Ali, S.M. / Bajpai, S.N. / Brouillette, W.J. / Air, G.M. / Luo, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vcj.cif.gz | 91.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vcj.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 1vcj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/1vcj ftp://data.pdbj.org/pub/pdb/validation_reports/vc/1vcj | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43331.234 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN RESIDUES 78-466 / Source method: isolated from a natural source / Source: (natural) Influenza B virus (B/Lee/40) / Genus: Influenzavirus BInfluenza B virus / Species: Influenza B virus / Strain: B-LEE-40 / References: UniProt: P03474, exo-alpha-sialidase |
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#2: Chemical | ChemComp-IBA / |
#3: 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: 3.12 Å3/Da / Density % sol: 60.28 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG 3350, sodium chloride, sodium nitrate, calcium chloride, sodium azide, pH 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.8 / Method: vapor diffusion, hanging drop / Details: Sudbeck, E.A., (1997) J. Mol. Biol., 267, 584. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 6, 1999 |
Radiation | Monochromator: graphite monochromator, 0.3 mm pinhole collimator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→25 Å / Num. all: 20397 / Num. obs: 18434 / % possible obs: 81.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rsym value: 0.084 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.207 / % possible all: 63.2 |
Reflection | *PLUS Highest resolution: 2.4 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / % possible obs: 63.2 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→6 Å / Cross valid method: THROUGHUOT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å /
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Refinement | *PLUS Rfactor Rfree: 0.253 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |