[English] 日本語
Yorodumi- PDB-1inv: A SIALIC ACID DERIVED PHOSPHONATE ANALOG INHIBITS DIFFERENT STRAI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1inv | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | A SIALIC ACID DERIVED PHOSPHONATE ANALOG INHIBITS DIFFERENT STRAINS OF INFLUENZA VIRUS NEURAMINIDASE WITH DIFFERENT EFFICIENCIES | |||||||||
Components | INFLUENZA VIRUS B/LEE/40 NEURAMINIDASE | |||||||||
Keywords | HYDROLASE / O-GLYCOSYL / NEURAMINIDASE / SIALIDASE | |||||||||
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 / Resolution: 2.4 Å | |||||||||
Authors | White, C.L. / Janakiraman, M.N. / Laver, W.G. / Philippon, C. / Vasella, A. / Air, G.M. / Luo, M. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: A sialic acid-derived phosphonate analog inhibits different strains of influenza virus neuraminidase with different efficiencies. Authors: White, C.L. / Janakiraman, M.N. / Laver, W.G. / Philippon, C. / Vasella, A. / Air, G.M. / Luo, M. #1: Journal: Biochemistry / Year: 1994 Title: Structure of Influenza Virus Neuraminidase B(Slash)Lee(Slash)40 Complexed with Sialic Acid and a Dehydro Analog at 1.8 Angstroms Resolution: Implications for the Catalytic Mechanism Authors: Janakiraman, M.N. / White, C.L. / Laver, W.G. / Air, G.M. / Luo, M. #2: Journal: J.Mol.Biol. / Year: 1991 Title: Three-Dimensional Structure of the Influenza Virus A(Slash)Tokyo(Slash)3(Slash)67 at 2.2 Angstroms Resolution Authors: Varghese, J.N. / Colman, P.M. #3: Journal: J.Mol.Biol. / Year: 1991 Title: Refined Atomic Structures of N9 Subtype Influenza Virus Neuraminidase and Escape Mutants Authors: Lip, W.R. / Varghese, J.N. / Baker, A.T. / Van Danelaar, A. / Laver, W.G. / Webster, R.G. / Colman, P.M. #4: Journal: Helv.Chim.Acta / Year: 1990 Title: Phosphonic-Acid Analogs of the N-Acetyl-2-Deoxyneuraminic Acids: Synthesis and Inhibition of Vibrio Choleae Sialidase Authors: Walliman, K. / Vasella, A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1inv.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1inv.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 1inv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/1inv ftp://data.pdbj.org/pub/pdb/validation_reports/in/1inv | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: CIS PROLINE - PRO 139 / 2: CIS PROLINE - PRO 326 | ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 43460.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus / Genus: Influenzavirus BInfluenza B virus / Cell line: 293 / Strain (production host): 293 / References: UniProt: P03474, exo-alpha-sialidase | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Sugar | ChemComp-NAG / | ||||||||
#3: Chemical | #4: Sugar | ChemComp-EQP / ( | #5: Water | ChemComp-HOH / | Nonpolymer details | TWO CALCIUMS ATOMS ARE INCLUDED IN THE REFINED STRUCTURE. RESIDUE CA 467 STABILIZES A LOOP NEAR THE ...TWO CALCIUMS ATOMS ARE INCLUDED IN THE REFINED STRUCTURE. RESIDUE CA 467 STABILIZES | Source details | EPANA SEE WALLIMAN & VASELLA (1990) FOR SYNTHESIS. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.74 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Details: NATIVE CRYSTALS SOAKED IN 10MM EPANA SOLUTION, PH 7.4. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 17019 / % possible obs: 72.3 % / Observed criterion σ(I): 2 |
Reflection | *PLUS Highest resolution: 2.38 Å / Lowest resolution: 9999 Å / Redundancy: 2.23 % / Rmerge(I) obs: 0.0967 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.4→8 Å / σ(F): 2 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.154 / Rfactor Rwork: 0.154 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|