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Yorodumi- PDB-2chw: A pharmacological map of the PI3-K family defines a role for p110... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2chw | ||||||
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Title | A pharmacological map of the PI3-K family defines a role for p110 alpha in signaling: The structure of complex of phosphoinositide 3- kinase gamma with inhibitor PIK-39 | ||||||
Components | PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT GAMMA ISOFORM | ||||||
Keywords | TRANSFERASE/INHIBITOR / COMPLEX TRANSFERASE-INHIBITOR / PHOSPHOINOSITIDE / KINASE / LIPID / INHIBITOR / 3-KINASE / SIGNALING / QUINAZOLINONE / TRANSFERASE / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information secretory granule localization / negative regulation of triglyceride catabolic process / natural killer cell chemotaxis / neutrophil extravasation / phosphatidylinositol-4-phosphate 3-kinase / regulation of calcium ion transmembrane transport / positive regulation of acute inflammatory response / respiratory burst involved in defense response / negative regulation of cardiac muscle contraction / T cell chemotaxis ...secretory granule localization / negative regulation of triglyceride catabolic process / natural killer cell chemotaxis / neutrophil extravasation / phosphatidylinositol-4-phosphate 3-kinase / regulation of calcium ion transmembrane transport / positive regulation of acute inflammatory response / respiratory burst involved in defense response / negative regulation of cardiac muscle contraction / T cell chemotaxis / negative regulation of fibroblast apoptotic process / phosphatidylinositol 3-kinase complex, class IB / sphingosine-1-phosphate receptor signaling pathway / dendritic cell chemotaxis / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / phosphatidylinositol 3-kinase / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / mast cell degranulation / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hepatocyte apoptotic process / positive regulation of Rac protein signal transduction / regulation of cell adhesion mediated by integrin / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / regulation of angiogenesis / T cell proliferation / cellular response to cAMP / GPVI-mediated activation cascade / T cell activation / ephrin receptor binding / neutrophil chemotaxis / positive regulation of endothelial cell migration / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cytokine production / positive regulation of MAP kinase activity / platelet aggregation / endocytosis / G beta:gamma signalling through PI3Kgamma / Signaling by CSF1 (M-CSF) in myeloid cells / kinase activity / positive regulation of cytosolic calcium ion concentration / angiogenesis / adaptive immune response / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / protein kinase activity / immune response / inflammatory response / G protein-coupled receptor signaling pathway / phosphorylation / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Knight, Z.A. / Gonzalez, B. / Feldman, M.E. / Zunder, E.R. / Goldenberg, D.D. / Williams, O. / Loewith, R. / Stokoe, D. / Balla, A. / Toth, B. ...Knight, Z.A. / Gonzalez, B. / Feldman, M.E. / Zunder, E.R. / Goldenberg, D.D. / Williams, O. / Loewith, R. / Stokoe, D. / Balla, A. / Toth, B. / Balla, T. / Weiss, W.A. / Williams, R.L. / Shokat, K.M. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2006 Title: A Pharmacological Map of the Pi3-K Family Defines a Role for P110Alpha in Signaling Authors: Knight, Z.A. / Gonzalez, B. / Feldman, M.E. / Zunder, E.R. / Goldenberg, D.D. / Williams, O. / Loewith, R. / Stokoe, D. / Balla, A. / Toth, B. / Balla, T. / Weiss, W.A. / Williams, R.L. / Shokat, K.M. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2chw.cif.gz | 184.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2chw.ent.gz | 142.6 KB | Display | PDB format |
PDBx/mmJSON format | 2chw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/2chw ftp://data.pdbj.org/pub/pdb/validation_reports/ch/2chw | HTTPS FTP |
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-Related structure data
Related structure data | 2chxC 2chzC 1e8zS S: Starting model for refinement 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
#1: Protein | Mass: 110756.164 Da / Num. of mol.: 1 Fragment: HUMAN PI-3K GAMMA CATALYTIC SUBUNIT, RESIDUES 144-1102 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PVL1393 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 References: UniProt: P48736, phosphatidylinositol 3-kinase, phosphatidylinositol-4,5-bisphosphate 3-kinase |
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#2: Chemical | ChemComp-039 / |
#3: 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: 2.4 Å3/Da / Density % sol: 40 % |
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Crystal grow | Method: vapor diffusion / pH: 7.5 Details: VAPOUR DIFFUSION 1 MICROLITER PROTEIN PLUS 1 MICROLITER RESERVOIR RESERVOIR: 17% PEG 4000, 250 MM AMMONIUM SULFATE AND 100 MM TRIS PH 7.5 PROTEIN: 4 MG/ML IN 0.5 MM AMMONIUM SULFATE, 20 MM ...Details: VAPOUR DIFFUSION 1 MICROLITER PROTEIN PLUS 1 MICROLITER RESERVOIR RESERVOIR: 17% PEG 4000, 250 MM AMMONIUM SULFATE AND 100 MM TRIS PH 7.5 PROTEIN: 4 MG/ML IN 0.5 MM AMMONIUM SULFATE, 20 MM TRIS PH 7.2, 1% ETHYLENE GLYCOL, 0.02% CHAPS AND 5 MM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 5, 2005 / Details: TORROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→62.14 Å / Num. obs: 31445 / % possible obs: 99.9 % / Observed criterion σ(I): -3.7 / Redundancy: 3.68 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.72 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.15 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E8Z Resolution: 2.6→62.14 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.889 / SU B: 34.088 / SU ML: 0.355 / Cross valid method: THROUGHOUT / ESU R: 0.983 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.69 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→62.14 Å
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