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Open data
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Basic information
Entry | Database: PDB / ID: 1uu3 | ||||||
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Title | Structure of human PDK1 kinase domain in complex with LY333531 | ||||||
![]() | 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 | ||||||
![]() | TRANSFERASE / PROTEIN KINASE / PKB / PDK1 / INHIBITOR / LY333531 / DIABETES / CANCER / SERINE/THREONINE-PROTEIN KINASE | ||||||
Function / homology | ![]() 3-phosphoinositide-dependent protein kinase activity / Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / positive regulation of phospholipase activity / RSK activation / hyperosmotic response / regulation of canonical NF-kappaB signal transduction / positive regulation of vascular endothelial cell proliferation ...3-phosphoinositide-dependent protein kinase activity / Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / positive regulation of phospholipase activity / RSK activation / hyperosmotic response / regulation of canonical NF-kappaB signal transduction / positive regulation of vascular endothelial cell proliferation / negative regulation of cardiac muscle cell apoptotic process / phospholipase activator activity / positive regulation of sprouting angiogenesis / Constitutive Signaling by AKT1 E17K in Cancer / CD28 dependent PI3K/Akt signaling / phospholipase binding / positive regulation of blood vessel endothelial cell migration / Role of LAT2/NTAL/LAB on calcium mobilization / Estrogen-stimulated signaling through PRKCZ / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of endothelial cell apoptotic process / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / extrinsic apoptotic signaling pathway / RHO GTPases activate PKNs / cellular response to epidermal growth factor stimulus / GPVI-mediated activation cascade / T cell costimulation / activation of protein kinase B activity / Integrin signaling / insulin-like growth factor receptor signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / cell projection / calcium-mediated signaling / positive regulation of protein localization to plasma membrane / peptidyl-threonine phosphorylation / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of protein kinase activity / epidermal growth factor receptor signaling pathway / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / G beta:gamma signalling through PI3Kgamma / cellular response to insulin stimulus / positive regulation of angiogenesis / Regulation of TP53 Degradation / cell migration / Downstream TCR signaling / insulin receptor signaling pathway / PIP3 activates AKT signaling / cytoplasmic vesicle / actin cytoskeleton organization / protein autophosphorylation / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Komander, D. / Kular, G.S. / Schuttelkopf, A.W. / Deak, M. / Prakash, K.R. / Bain, J. / Elliot, M. / Garrido-Franco, M. / Kozikowski, A.P. / Alessi, D.R. / Van Aalten, D.M.F. | ||||||
![]() | ![]() Title: Interactions of Ly333531 and Other Bisindolyl Maleimide Inhibitors with Pdk1 Authors: Komander, D. / Kular, G.S. / Schuttelkopf, A.W. / Deak, M. / Prakash, K.R. / Bain, J. / Elliot, M. / Garrido-Franco, M. / Kozikowski, A.P. / Alessi, D.R. / Van Aalten, D.M.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.3 KB | Display | ![]() |
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PDB format | ![]() | 61.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 883.7 KB | Display | ![]() |
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Full document | ![]() | 888.5 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 24.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1uu7C ![]() 1uu8C ![]() 1uu9C ![]() 1uvrC ![]() 1h1wS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 35498.688 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 51-360 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-LY4 / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 2.1 M AMMONIUM SULPHATE 0.1 M TRIS-HCL PH 7.2 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→25 Å / Num. obs: 44644 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 4.7 / % possible all: 98.6 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 25 Å / Redundancy: 4.9 % / Num. measured all: 218856 / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 98.6 % / Redundancy: 3.7 % / Num. unique obs: 4344 / Num. measured obs: 15901 / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 4.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1H1W Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.428 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS SOME SIDECHAINS REFINED WITH OCCUPANCY = 0.00 DUE TO DISORDER. SOME RESIDUES MUTATED TO ALANINE DUE TO DISORDER.
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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: 17.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→25 Å
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Refine LS restraints |
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