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- PDB-2x38: The crystal structure of the murine class IA PI 3-kinase p110delt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2x38 | |||||||||
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Title | The crystal structure of the murine class IA PI 3-kinase p110delta in complex with IC87114. | |||||||||
![]() | PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT DELTA ISOFORM | |||||||||
![]() | TRANSFERASE / PHOSPHOINOSITIDE 3-KINASE / ISOFORM-SPECIFIC INHIBITORS / CANCER | |||||||||
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 / cell migration / kinase activity / adaptive immune response / cell surface receptor signaling pathway / cell differentiation / inflammatory response / phosphorylation / 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 | ![]() ![]() ![]() | |||||||||
![]() | Berndt, A. / Miller, S. / Williams, O. / Lee, D.D. / Houseman, B.T. / Pacold, J.I. / Gorrec, F. / Hon, W.-C. / Liu, Y. / Rommel, C. ...Berndt, A. / Miller, S. / Williams, O. / Lee, D.D. / Houseman, B.T. / Pacold, J.I. / Gorrec, F. / Hon, W.-C. / Liu, Y. / Rommel, C. / Gaillard, P. / Ruckle, T. / Schwarz, M.K. / Shokat, K.M. / Shaw, J.P. / Williams, R.L. | |||||||||
![]() | ![]() Title: The P110D Structure: Mechanisms for Selectivity and Potency of New Pi(3)K Inhibitors Authors: Berndt, A. / Miller, S. / Williams, O. / Lee, D.D. / Houseman, B.T. / Pacold, J.I. / Gorrec, F. / Hon, W.-C. / Liu, Y. / Rommel, C. / Gaillard, P. / Ruckle, T. / Schwarz, M.K. / Shokat, K.M. ...Authors: Berndt, A. / Miller, S. / Williams, O. / Lee, D.D. / Houseman, B.T. / Pacold, J.I. / Gorrec, F. / Hon, W.-C. / Liu, Y. / Rommel, C. / Gaillard, P. / Ruckle, T. / Schwarz, M.K. / Shokat, K.M. / Shaw, J.P. / Williams, R.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 | ![]() | 179.7 KB | Display | ![]() |
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PDB format | ![]() | 137.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 827 KB | Display | ![]() |
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Full document | ![]() | 841.4 KB | Display | |
Data in XML | ![]() | 29.8 KB | Display | |
Data in CIF | ![]() | 41.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wxfC ![]() 2wxgC ![]() 2wxhC ![]() 2wxiC ![]() 2wxjC ![]() 2wxkC ![]() 2wxlC ![]() 2wxmC ![]() 2wxnC ![]() 2wxoC ![]() 2wxpC ![]() 2wxqC ![]() 2wxrC ![]() 2rd0S S: Starting model for refinement 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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Unit cell |
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Components
#1: Protein | Mass: 107823.664 Da / Num. of mol.: 1 / Fragment: RESIDUES 106-1044 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q3UDT3, UniProt: O35904*PLUS, phosphatidylinositol-4,5-bisphosphate 3-kinase |
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#2: Chemical | ChemComp-IC8 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.76 % / Description: NONE |
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Crystal grow | pH: 6.8 Details: 20% (V/V) GLYCEROL, 10% (V/V) PEG 4K, 30 MM NANO3, 30 MM NA2HPO4, 30 MM (NH4)2SO4, 100 MM IMIDAZOLE PH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 21, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→56.89 Å / Num. obs: 51811 / % possible obs: 98.4 % / Observed criterion σ(I): -3.7 / Redundancy: 3.53 % / Biso Wilson estimate: 37.612 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.92 |
Reflection shell | Resolution: 2.2→2.22 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.62 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2RD0 Resolution: 2.2→56.89 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.88 / SU B: 14.695 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
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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: 22.467 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→56.89 Å
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