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Yorodumi- PDB-1e8w: Structure determinants of phosphoinositide 3-kinase inhibition by... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e8w | ||||||
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Title | Structure determinants of phosphoinositide 3-kinase inhibition by wortmannin, LY294002, quercetin, myricetin and staurosporine | ||||||
Components | PHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT | ||||||
Keywords | PHOSPHOINOSITIDE 3-KINASE GAMMA / SECONDARY MESSENGER GENERATION / PI3K / PI 3K / QUERCETIN | ||||||
Function / homology | Function and homology information phosphatidylinositol-4-phosphate 3-kinase / phosphatidylinositol 3-kinase complex, class IB / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / immune system process ...phosphatidylinositol-4-phosphate 3-kinase / phosphatidylinositol 3-kinase complex, class IB / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / immune system process / phosphatidylinositol phosphate biosynthetic process / phosphatidylinositol 3-kinase/protein kinase B signal transduction / endocytosis / chemotaxis / angiogenesis / non-specific serine/threonine protein kinase / inflammatory response / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | SUS SCROFA (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Walker, E.H. / Pacold, M.E. / Perisic, O. / Stephens, L. / Hawkins, P.T. / Wymann, M.P. / Williams, R.L. | ||||||
Citation | Journal: Mol.Cell / Year: 2000 Title: Structural Determinations of Phosphoinositide 3-Kinase Inhibition by Wortmannin, Ly294002, Quercetin, Myricetin and Staurosporine Authors: Walker, E.H. / Pacold, M.E. / Perisic, O. / Stephens, L. / Hawkins, P.T. / Whymann, M.P. / Williams, R.L. #1: Journal: Nature / Year: 1999 Title: Structural Insights Into Phosphoinositide 3-Kinase Catalysis and Signalling Authors: Walker, E.H. / Perisic, O. / Ried, C. / Stephens, L. / Williams, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e8w.cif.gz | 185.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e8w.ent.gz | 144.7 KB | Display | PDB format |
PDBx/mmJSON format | 1e8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/1e8w ftp://data.pdbj.org/pub/pdb/validation_reports/e8/1e8w | HTTPS FTP |
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-Related structure data
Related structure data | 1e7uC 1e7vC 1e8xC 1e8yC 1e8zC 1e90C 1qmm C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 109952.555 Da / Num. of mol.: 1 / Fragment: PI3-KINASE P110 SUBUNIT GAMMA / Mutation: YES Source method: isolated from a genetically manipulated source Details: QUERCETIN / Source: (gene. exp.) SUS SCROFA (pig) / Cell: NEUTROPHIL / Gene: P120S144C / Plasmid: PACHLT-C / Gene (production host): P120S144C / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): Sf9 / References: UniProt: O02697, phosphatidylinositol 3-kinase |
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#2: Chemical | ChemComp-QUE / |
Sequence details | THE NATIVE PROTEIN WAS MUTATED BY DELETION OF RESIDUES 1-143. THE RESIDUE 143 LISTED HERE IS FROM ...THE NATIVE PROTEIN WAS MUTATED BY DELETION OF RESIDUES 1-143. THE RESIDUE 143 LISTED HERE IS FROM THE HIS-TAG, AFTER THROMBIN CLEAVAGE. ALSO RESEQUENCI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.829 Å3/Da / Density % sol: 54.85 % | ||||||||||||||||||||
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Crystal grow | pH: 7.25 / Details: 14% PEG 4000, 0.2 M LI2SO4, 0.1 M TRIS PH 7.25 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop / Details: used hair seeding | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 15, 1999 / Details: BENT MIRROR |
Radiation | Monochromator: DIAMOND C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→62.45 Å / Num. obs: 34614 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3.37 % / Biso Wilson estimate: 57.3 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 22.55 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.51 / Rsym value: 0.397 / % possible all: 83.1 |
Reflection | *PLUS Num. measured all: 116715 |
Reflection shell | *PLUS % possible obs: 83.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QMM 1qmm Resolution: 2.5→62.45 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1791131.55 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.5134 Å2 / ksol: 0.337475 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→62.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.33 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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