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- PDB-2wxm: 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: 2wxm | ||||||
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Title | The crystal structure of the murine class IA PI 3-kinase p110delta in complex with DL06. | ||||||
![]() | PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT DELTA ISOFORM | ||||||
![]() | TRANSFERASE / PHOSPHOPROTEIN / 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 / 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 / cytosol / cytoplasm 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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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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 178.7 KB | Display | ![]() |
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PDB format | ![]() | 137.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2wxfC ![]() 2wxgC ![]() 2wxhC ![]() 2wxiC ![]() 2wxjC ![]() 2wxkC ![]() 2wxlC ![]() 2wxnC ![]() 2wxoC ![]() 2wxpC ![]() 2wxqC ![]() 2wxrC ![]() 2x38C ![]() 2rd0S C: citing same article ( S: Starting model for refinement |
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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-ZZM / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.19 % / Description: NONE |
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Crystal grow | pH: 6.8 Details: 20% (V/V) GLYCEROL, 10% (W/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: Aug 31, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→58.62 Å / Num. obs: 25680 / % possible obs: 98.9 % / Observed criterion σ(I): -3.7 / Redundancy: 3.32 % / Biso Wilson estimate: 59.76 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.95 |
Reflection shell | Resolution: 2.8→2.82 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.42 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2RD0 Resolution: 2.8→58.62 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.826 / SU B: 40.994 / SU ML: 0.369 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.421 / 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: 20.557 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→58.62 Å
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