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Yorodumi- PDB-1bji: THE X-RAY STRUCTURE OF A COMPLEX OF TERN N9 INFLUENZA VIRUS NEURA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bji | |||||||||
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Title | THE X-RAY STRUCTURE OF A COMPLEX OF TERN N9 INFLUENZA VIRUS NEURAMINIDASE COMPLEXED WITH THE GLAXO 6-CARBOXAMIDE SIALIC ACID ANALOGUE GR217029 | |||||||||
Components | NEURAMINIDASE | |||||||||
Keywords | NEURAMINIDASE / INFLUENZA PROTEIN / INHIBITOR COMPLEX / 6-CARBOXAMIDE DERIVATIVE / SIALIC ACID ANALOGUE / GLAXO GR217029 / HYDROLASE / GLYCOPROTEIN | |||||||||
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 / Resolution: 2 Å | |||||||||
Authors | Varghese, J.N. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 1998 Title: Dihydropyrancarboxamides related to zanamivir: a new series of inhibitors of influenza virus sialidases. 2. Crystallographic and molecular modeling study of complexes of 4-amino-4H-pyran-6- ...Title: Dihydropyrancarboxamides related to zanamivir: a new series of inhibitors of influenza virus sialidases. 2. Crystallographic and molecular modeling study of complexes of 4-amino-4H-pyran-6-carboxamides and sialidase from influenza virus types A and B. Authors: Taylor, N.R. / Cleasby, A. / Singh, O. / Skarzynski, T. / Wonacott, A.J. / Smith, P.W. / Sollis, S.L. / Howes, P.D. / Cherry, P.C. / Bethell, R. / Colman, P. / Varghese, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bji.cif.gz | 99.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bji.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bji_validation.pdf.gz | 562.9 KB | Display | wwPDB validaton report |
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Full document | 1bji_full_validation.pdf.gz | 571.7 KB | Display | |
Data in XML | 1bji_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 1bji_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/1bji ftp://data.pdbj.org/pub/pdb/validation_reports/bj/1bji | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43723.770 Da / Num. of mol.: 1 / Fragment: RESIDUES 82 - 468 / Source method: isolated from a natural source / Details: DETERGENT RELEASED, PRONASE DIGESTED / Source: (natural) Influenza A virus / Genus: Influenzavirus A / Strain: A/TERN/AUSTRALIA/G70C/75 / References: UniProt: P03472, exo-alpha-sialidase |
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-Sugars , 4 types, 5 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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 | ChemComp-MAN / | ||
#4: Sugar | #6: Sugar | ChemComp-DPC / | |
-Non-polymers , 2 types, 192 molecules
#5: Chemical | ChemComp-CA / |
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#7: 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: 2.91 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||
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Crystal grow | pH: 7 Details: 1.9M PHOSPHATE(PH 5.9) THE GLAXO 6-CARBOXAMIDE COMPOUND GR217029 WAS SOAKED IN TERN N9 NEURAMININDASE CRYSTALS AT 5 MM FOR 24HR. THIS EXPERIMENT WAS CARRIED OUT TO DETERMINE THE BINDING MODE ...Details: 1.9M PHOSPHATE(PH 5.9) THE GLAXO 6-CARBOXAMIDE COMPOUND GR217029 WAS SOAKED IN TERN N9 NEURAMININDASE CRYSTALS AT 5 MM FOR 24HR. THIS EXPERIMENT WAS CARRIED OUT TO DETERMINE THE BINDING MODE OF THE 6-CARBOXAMIDE HYDROPHOBIC GROUP. A NEW HYDROPHOBIC POCKET WAS DISCOVERED EARLIER WITH A METHYL, ETHYL GROUP ATTACHED TO THE AMIDE OF TH3E SIX-CARBOXAMIDE. THIS COMPOUND HAS A MUCH LARGER HYDROPHOBIC GROUP ATTACHED., pH 7.0 | ||||||||||||||||||||
Crystal grow | *PLUS pH: 6.6 / Method: vapor diffusion / Details: Laver, W.G., (1984) Virology, 137, 314. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 10, 1994 / Details: YALE MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→100 Å / Num. obs: 119194 / % possible obs: 68 % / Observed criterion σ(I): 2 / Redundancy: 5.07 % / Rmerge(I) obs: 0.096 / Rsym value: 0.084 |
Reflection shell | Resolution: 2.012→2.151 Å / % possible all: 27 |
Reflection | *PLUS Num. obs: 23918 / Num. measured all: 119194 |
Reflection shell | *PLUS % possible obs: 27 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: TERN N9 NEURAMINIDASE Resolution: 2→6 Å / σ(F): 2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.04 Å / Total num. of bins used: 15 / % reflection obs: 24 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 20.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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