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Yorodumi- PDB-1l7f: Crystal structure of influenza virus neuraminidase in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l7f | |||||||||
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Title | Crystal structure of influenza virus neuraminidase in complex with BCX-1812 | |||||||||
Components | neuraminidase | |||||||||
Keywords | HYDROLASE / N9 neuraminidase / influenza / glycosylated protein / BCX-1812 | |||||||||
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: 1.8 Å | |||||||||
Authors | Smith, B.J. / McKimm-Breshkin, J.L. / McDonald, M. / Fernley, R.T. / Varghese, J.N. / Colman, P.M. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2002 Title: Structural studies of the resistance of influenza virus neuramindase to inhibitors. Authors: Smith, B.J. / McKimm-Breshkin, J.L. / McDonald, M. / Fernley, R.T. / Varghese, J.N. / Colman, P.M. #1: Journal: Protein Sci. / Year: 1995 Title: Three-dimensional structure of the complex of 4-guanidino-Neu5Ac2en and influenza virus neuraminidase Authors: Varghese, J.N. / Epa, V.C. / Colman, P.M. #2: Journal: Structure / Year: 1998 Title: Drug design against a shifting target: a structural basis for resistance to inhibitors in a variant of influenza virus neuraminidase Authors: Varghese, J.N. / Smith, P.W. / Sollis, S.L. / Blick, T.J. / Sahasrabudhe, A. / McKimm-Breschkin, J.L. / Colman, P.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l7f.cif.gz | 107.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l7f.ent.gz | 84.5 KB | Display | PDB format |
PDBx/mmJSON format | 1l7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l7f_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1l7f_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1l7f_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 1l7f_validation.cif.gz | 38.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/1l7f ftp://data.pdbj.org/pub/pdb/validation_reports/l7/1l7f | 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43723.770 Da / Num. of mol.: 1 Fragment: integral membrane protein, membrane stalk cleaved by pronase releasing fully active residues 82-468 Source method: isolated from a natural source / Source: (natural) Influenza A virus / Genus: Influenzavirus A / Strain: A/NWS/Tern/Australia/G70C/75 / References: UniProt: P03472, exo-alpha-sialidase |
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-Sugars , 3 types, 3 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: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 648 molecules
#5: Chemical | #6: Chemical | ChemComp-BCZ / | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.53 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: phosphate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
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: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: elliptical glass monocapillary |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 46825 / % possible obs: 100 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.15 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.2 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 453337 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→6 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.865 Å
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Refinement | *PLUS Rfactor obs: 0.153 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_planar_d / Dev ideal: 0.023 |