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- PDB-1o6k: Structure of activated form of PKB kinase domain S474D with GSK3 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1o6k | ||||||
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Title | Structure of activated form of PKB kinase domain S474D with GSK3 peptide and AMP-PNP | ||||||
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![]() | TRANSFERASE / PROTEIN KINASE / SERINE/THREONINE-PROTEIN KINASE | ||||||
Function / homology | ![]() retinal rod cell apoptotic process / PDE3B signalling / cellular response to high light intensity / Inhibition of TSC complex formation by PKB / AKT-mediated inactivation of FOXO1A / Negative regulation of the PI3K/AKT network / negative regulation of long-chain fatty acid import across plasma membrane / Activation of AKT2 / AKT phosphorylates targets in the nucleus / regulation of microtubule anchoring at centrosome ...retinal rod cell apoptotic process / PDE3B signalling / cellular response to high light intensity / Inhibition of TSC complex formation by PKB / AKT-mediated inactivation of FOXO1A / Negative regulation of the PI3K/AKT network / negative regulation of long-chain fatty acid import across plasma membrane / Activation of AKT2 / AKT phosphorylates targets in the nucleus / regulation of microtubule anchoring at centrosome / negative regulation of glycogen (starch) synthase activity / neuron projection organization / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / negative regulation of type B pancreatic cell development / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / RUNX2 regulates genes involved in cell migration / negative regulation of dopaminergic neuron differentiation / : / maintenance of cell polarity / positive regulation of protein localization to centrosome / : / positive regulation of fatty acid beta-oxidation / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of cilium assembly / mammary gland epithelial cell differentiation / negative regulation of protein acetylation / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / beta-catenin destruction complex / RAB GEFs exchange GTP for GDP on RABs / positive regulation of glucose metabolic process / tau-protein kinase / CRMPs in Sema3A signaling / heart valve development / regulation of microtubule-based process / regulation of protein export from nucleus / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / peripheral nervous system myelin maintenance / Maturation of nucleoprotein / cellular response to interleukin-3 / Wnt signalosome / negative regulation of protein localization to nucleus / positive regulation of cell motility / glycogen biosynthetic process / negative regulation of TOR signaling / regulation of long-term synaptic potentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Maturation of nucleoprotein / AKT phosphorylates targets in the cytosol / negative regulation of calcineurin-NFAT signaling cascade / positive regulation of cell-matrix adhesion / regulation of axon extension / G protein-coupled dopamine receptor signaling pathway / Regulation of TP53 Activity through Association with Co-factors / negative regulation of phosphoprotein phosphatase activity / regulation of dendrite morphogenesis / establishment of cell polarity / regulation of axonogenesis / tau-protein kinase activity / CTLA4 inhibitory signaling / glycogen metabolic process / ER overload response / fat cell differentiation / Constitutive Signaling by AKT1 E17K in Cancer / protein kinase A catalytic subunit binding / dynactin binding / CD28 dependent PI3K/Akt signaling / Regulation of localization of FOXO transcription factors / NF-kappaB binding / positive regulation of glycogen biosynthetic process / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Regulation of HSF1-mediated heat shock response / Activation of BAD and translocation to mitochondria / positive regulation of protein targeting to membrane / epithelial to mesenchymal transition / negative regulation of osteoblast differentiation / canonical Wnt signaling pathway / negative regulation of protein-containing complex assembly / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / positive regulation of autophagy / Cyclin E associated events during G1/S transition / regulation of microtubule cytoskeleton organization / regulation of cellular response to heat / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway in absence of ligand / regulation of cell migration / Regulation of TP53 Activity through Acetylation / presynaptic modulation of chemical synaptic transmission Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, J. / Cron, P. / Good, V.M. / Thompson, V. / Hemmings, B.A. / Barford, D. | ||||||
![]() | ![]() Title: Crystal Structure of an Activated Akt/Protein Kinase B Ternary Complex with Gsk-3 Peptide and AMP-Pnp Authors: Yang, J. / Cron, P. / Good, V.M. / Thompson, V. / Hemmings, B.A. / Barford, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.7 KB | Display | ![]() |
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PDB format | ![]() | 65.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 791.4 KB | Display | ![]() |
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Full document | ![]() | 794.1 KB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 25.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | CHAIN A IS A MONOMER, BUT THIS ENTRY IS CLASSIFIEDAS A DIMER AS CHAIN A IS IN COMPLEX WITH A PEPTIDE(CHAIN C), FORMING A DIMERIC ASSOCIATION. |
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Components
#1: Protein | Mass: 39121.645 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 146-481 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P31751, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor | ||||
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#2: Protein/peptide | Mass: 1123.220 Da / Num. of mol.: 1 / Fragment: PEPTIDE, RESIDUES 3-12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
#3: Chemical | ChemComp-ANP / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Compound details | PROTEIN KINASE KNOWN TO PHOSPHORYL | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 10 MG/ML PROTEIN 20 PEG 4K, 10% ISOPROPONAL, 5 MM DTT, pH 7.50 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||
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: Jul 15, 2002 |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 116971 / % possible obs: 82.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.7→1.8 Å / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 2.3 / % possible all: 63.7 |
Reflection | *PLUS Highest resolution: 1.7 Å / Num. obs: 27820 / Num. measured all: 116971 |
Reflection shell | *PLUS Lowest resolution: 1.79 Å / % possible obs: 63.7 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: CDK1 Resolution: 1.7→36.89 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1566941.48 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 17.395 Å2 / ksol: 0.337772 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→36.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 50 Å / % reflection Rfree: 3.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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