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Open data
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Basic information
Entry | Database: PDB / ID: 5t28 | ||||||
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Title | mPI3Kd IN COMPLEX WITH 5k | ||||||
![]() | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform | ||||||
![]() | TRANSFERASE / mI3Kd / inhibitor | ||||||
Function / homology | ![]() Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Interleukin receptor SHC signaling / Synthesis of PIPs at the plasma membrane / PIP3 activates AKT signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of signaling by CBL / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / RET signaling / phosphatidylinositol 3-kinase complex ...Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Interleukin receptor SHC signaling / Synthesis of PIPs at the plasma membrane / PIP3 activates AKT signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of signaling by CBL / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / RET signaling / phosphatidylinositol 3-kinase complex / 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 / B cell activation / phosphatidylinositol-mediated signaling / B cell homeostasis / homeostasis of number of cells / defense response to fungus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of angiogenesis / chemotaxis / kinase activity / adaptive immune response / cell differentiation / cell surface receptor signaling pathway / inflammatory response / negative regulation of gene expression / innate immune response / positive regulation of gene expression / ATP binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Petersen, J. / Terstige, I. / Perry, M. / Svensson, T. / Tyrchan, C. / Lindmark, H. / Oster, L. | ||||||
![]() | ![]() Title: Discovery of triazole aminopyrazines as a highly potent and selective series of PI3K delta inhibitors. Authors: Terstiege, I. / Perry, M. / Petersen, J. / Tyrchan, C. / Svensson, T. / Lindmark, H. / Oster, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.4 KB | Display | ![]() |
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PDB format | ![]() | 140.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5t23C ![]() 5t27C ![]() 5t2bC ![]() 5t2dC ![]() 5t2gC ![]() 5t2iC ![]() 5t2lC ![]() 5t2mC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 107766.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: Insect cell expression vector pTIE1 (others) References: UniProt: O35904, phosphatidylinositol-4,5-bisphosphate 3-kinase |
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#2: Chemical | ChemComp-74Q / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 50% ethylene glycol/PEG 8000, 0.1 M carboxylic acids mix, 0.1 M Buffer system 2 pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→56.14 Å / Num. obs: 25220 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 80.98 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 64.96 Å2
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Refine analyze | Luzzati coordinate error obs: 0.43 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→43.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
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