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Yorodumi- PDB-1iny: A SIALIC ACID DERIVED PHOSPHONATE ANALOG INHIBITS DIFFERENT STRAI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1iny | |||||||||
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Title | A SIALIC ACID DERIVED PHOSPHONATE ANALOG INHIBITS DIFFERENT STRAINS OF INFLUENZA VIRUS NEURAMINIDASE WITH DIFFERENT EFFICIENCIES | |||||||||
Components | INFLUENZA A SUBTYPE N9 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 A 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iny.cif.gz | 110.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iny.ent.gz | 89.7 KB | Display | PDB format |
PDBx/mmJSON format | 1iny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/1iny ftp://data.pdbj.org/pub/pdb/validation_reports/in/1iny | 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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Atom site foot note | 1: CIS PROLINE - PRO 327 / 2: CIS PROLINE - PRO 432 |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43749.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Genus: Influenzavirus A / References: UniProt: P03472, exo-alpha-sialidase |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#3: Sugar | #5: Sugar | ChemComp-EQP / ( | |
-Non-polymers , 2 types, 56 molecules
#4: Chemical | ChemComp-CA / |
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#6: Water | ChemComp-HOH / |
-Details
Nonpolymer details | THE CALCIUM RESIDUE, CA 470, STABILIZES A LOOP NEAR THE NEURAMINIDASE ACTIVE SITE. THE EQUATORIAL ...THE CALCIUM RESIDUE, CA 470, STABILIZES |
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Source details | EPANA SEE WALLIMAN & VASELLA (1990) FOR SYNTHESIS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.09 % |
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Crystal grow | Details: NATIVE CRYSTALS SOAKED IN 10MM EPANA SOLUTION, PH 7.2. |
Crystal grow | *PLUS pH: 6.6 / Method: vapor diffusion, hanging drop |
Components of the solutions | *PLUS Conc.: 1.7 M / Common name: potassium phosphate |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 20761 / % possible obs: 75.9 % / Observed criterion σ(I): 2 |
Reflection | *PLUS Highest resolution: 2.38 Å / Redundancy: 3.97 % / Rmerge(I) obs: 0.1657 |
-Processing
Software |
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Refinement | Resolution: 2.4→8 Å / σ(F): 2 /
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Displacement parameters | Biso mean: 12.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.187 / Rfactor Rwork: 0.187 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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