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Yorodumi- PDB-2v4l: complex of human phosphoinositide 3-kinase catalytic subunit gamm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v4l | ||||||
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Title | complex of human phosphoinositide 3-kinase catalytic subunit gamma (p110 gamma) with PIK-284 | ||||||
Components | PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT GAMMA ISOFORM | ||||||
Keywords | TRANSFERASE / LIPID KINASE / PHOSPHOINOSITIDE / PYRAZOLOPYRIMIDINE / S1 / KINASE / PIK-284 / 3-KINASE / INHIBITOR / SIGNALING | ||||||
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 / positive regulation of acute inflammatory response / respiratory burst involved in defense response / negative regulation of cardiac muscle contraction / regulation of calcium ion transmembrane transport / T cell chemotaxis ...secretory granule localization / negative regulation of triglyceride catabolic process / natural killer cell chemotaxis / neutrophil extravasation / phosphatidylinositol-4-phosphate 3-kinase / positive regulation of acute inflammatory response / respiratory burst involved in defense response / negative regulation of cardiac muscle contraction / regulation of calcium ion transmembrane transport / T cell chemotaxis / negative regulation of fibroblast apoptotic process / phosphatidylinositol 3-kinase complex, class IB / sphingosine-1-phosphate receptor signaling pathway / phosphatidylinositol 3-kinase complex, class IA / 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-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 / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / regulation of cell adhesion mediated by integrin / Synthesis of PIPs at the plasma membrane / regulation of angiogenesis / T cell proliferation / cellular response to cAMP / GPVI-mediated activation cascade / T cell activation / ephrin receptor binding / positive regulation of endothelial cell migration / neutrophil chemotaxis / 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 / inflammatory response / immune 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: 2.5 Å | ||||||
Authors | Apsel, B. / Gonzalez, B. / Blair, J.A. / Nazif, T.M. / Feldman, M.E. / Williams, R.L. / Shokat, K.M. / Knight, Z.A. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2008 Title: Targeted Polypharmacology: Discovery of Dual Inhibitors of Tyrosine and Phosphoinositide Kinases. Authors: Apsel, B. / Blair, J.A. / Gonzalez, B. / Nazif, T.M. / Feldman, M.E. / Aizenstein, B. / Hoffman, R. / Williams, R.L. / Shokat, K.M. / Knight, Z.A. | ||||||
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 | 2v4l.cif.gz | 185.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v4l.ent.gz | 143.3 KB | Display | PDB format |
PDBx/mmJSON format | 2v4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/2v4l ftp://data.pdbj.org/pub/pdb/validation_reports/v4/2v4l | HTTPS FTP |
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-Related structure data
Related structure data | 3en4C 3en5C 3en6C 3en7C 3eneC 2chxS 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: 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-4,5-bisphosphate 3-kinase |
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#2: Chemical | ChemComp-ABJ / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | 3-(4-AMINO-1-ISOPROPYL-1H-PYRAZOLO[3, 4-D]PYRIMIDIN-3-YL)PHENOL (284): THIS IS COMPOUND S1 IN THE ...3-(4-AMINO-1-ISOPROPYL-1H-PYRAZOLO[3, 4-D]PYRIMIDIN-3-YL)PHENOL (284): THIS IS COMPOUND S1 IN THE NAT CHEM BIOL PUBLICATIO |
Sequence details | RESIDUES 144-1102 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: RESERVOIR: 16-17% PEG 4000, 250 MM (NH4)2SO4 AND 100MM TRIS PH 7.5 PROTEIN: 4 MG/ML IN A BUFFER CONTAINING 0.5 MM (NH4)2SO4, 20 MM TRIS PH 7.2, 1% ETHYLENE GLYCOL, 0.02% CHAPS AND 5 MM DTT ...Details: RESERVOIR: 16-17% PEG 4000, 250 MM (NH4)2SO4 AND 100MM TRIS PH 7.5 PROTEIN: 4 MG/ML IN A BUFFER CONTAINING 0.5 MM (NH4)2SO4, 20 MM TRIS PH 7.2, 1% ETHYLENE GLYCOL, 0.02% CHAPS AND 5 MM DTT DROPS WERE 1MICROLITER PROTEIN PLUS 1 MICROLITER RESERVOIR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934 |
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: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→54.4 Å / Num. obs: 33672 / % possible obs: 99.7 % / Observed criterion σ(I): -3.7 / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.7 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CHX Resolution: 2.5→54.39 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.88 / SU B: 11.231 / SU ML: 0.257 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.681 / ESU R Free: 0.344 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.03 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→54.39 Å
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Refine LS restraints |
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