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Yorodumi- PDB-2qwk: THE X-RAY STRUCTURE OF A COMPLEX OF 5-N-ACETYL-5-AMINO-3-(1-ETHYL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qwk | |||||||||
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Title | THE X-RAY STRUCTURE OF A COMPLEX OF 5-N-ACETYL-5-AMINO-3-(1-ETHYLPROPOXY)-1-CYCLOHEXENE-1-CARBOXYLIC ACID (GS4071) AND WILDTYPE TERN N9 INFLUENZA VIRUS NEURAMINIDASE | |||||||||
Components | NEURAMINIDASE | |||||||||
Keywords | HYDROLASE / NEURAMINIDASE / INFLUENZA PROTEIN / SIALIC ACID ANALOGUES / DANA ANOLOGUES / GS4071. NEURAMINIDASE / DRUG RESISTANT VARIANT / GLYCOSYLATED PROTEIN / GS4071 | |||||||||
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 | Varghese, J.N. | |||||||||
Citation | 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. #1: Journal: J.Virol. / Year: 1998 Title: Mutations in a Conserved Residue in the Influenza Virus Neuraminidase Active Site Decreases Sensitivity to Neu5Ac2En-Derived Inhibitors Authors: Mckimm-Breschkin, J.L. / Sahasrabudhe, A. / Blick, T.J. / Mcdonald, M. / Colman, P.M. / Hart, G.J. / Bethell, R.C. / Varghese, J.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qwk.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qwk.ent.gz | 78.4 KB | Display | PDB format |
PDBx/mmJSON format | 2qwk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/2qwk ftp://data.pdbj.org/pub/pdb/validation_reports/qw/2qwk | HTTPS FTP |
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-Related structure data
Related structure data | 2qwaC 2qwbC 2qwcC 2qwdC 2qweC 2qwfC 2qwgC 2qwhC 2qwiC 2qwjC C: citing same article (ref.) |
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Similar 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: RESIDUES 82 - 468 Source method: isolated from a genetically manipulated source Details: INTEGRAL MEMBRANE PROTEIN, MEMBRANE BOUND STALK CLEAVED BY PRONASE, RELEASING FULLY ACTIVE HEAD WITH RESIDUES 82 - 468 (TOKYO/3/67 NUMBERING) Source: (gene. exp.) Influenza A virus / Genus: Influenzavirus A / Strain: A/TERN/AUSTRALIA/G70C/75 / Production host: Gallus gallus (chicken) / 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 , 3 types, 353 molecules
#5: Chemical | ChemComp-G39 / ( | ||
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#6: Chemical | #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: 2.82 Å3/Da / Density % sol: 54 % Description: THIS EXPERIMENT WAS CARRIED OUT TO DETERMINE THE STRUCTURE OF COMPLEX OF 5-N-ACETYL-5-AMINO-3- (1-ETHYLPROPOXY)-1-CYCLOHEXENE-1-CARBOXYLIC ACID (GS4071) AND WILDTYPE TERN N9 NEURAMINIDASE. | ||||||||||||||||||||
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Crystal grow | pH: 5.9 / Details: 1.9M PHOSPHATE (PH 5.9) | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
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: 107 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 13, 1997 / Details: YALE MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100 Å / Num. obs: 37216 / % possible obs: 79.6 % / Observed criterion σ(I): 1 / Redundancy: 4.15 % / Rmerge(I) obs: 0.092 / Rsym value: 0.088 |
Reflection shell | Resolution: 1.8→1.863 Å / % possible all: 29.5 |
Reflection | *PLUS Num. measured all: 154336 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: TERN N9 NEURAMINIDASE Resolution: 1.8→6 Å / σ(F): 1 / Details: 2 METAL IONS
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Refine analyze | Luzzati coordinate error obs: 0.01 Å / Luzzati d res low obs: 6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→1.83 Å / Total num. of bins used: 20
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: V3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |