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- PDB-1gzk: Molecular mechanism for the regulation of protein kinase B/Akt by... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gzk | ||||||
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Title | Molecular mechanism for the regulation of protein kinase B/Akt by hydrophobic motif phosphorylation | ||||||
![]() | RAC-BETA SERINE/THREONINE PROTEIN KINASE | ||||||
![]() | KINASE / TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING | ||||||
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 / RUNX2 regulates genes involved in cell migration ...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 / RUNX2 regulates genes involved in cell migration / : / positive regulation of fatty acid beta-oxidation / mammary gland epithelial cell differentiation / RAB GEFs exchange GTP for GDP on RABs / positive regulation of glucose metabolic process / peripheral nervous system myelin maintenance / positive regulation of cell motility / glycogen biosynthetic process / AKT phosphorylates targets in the cytosol / Regulation of TP53 Activity through Association with Co-factors / CTLA4 inhibitory signaling / fat cell differentiation / Constitutive Signaling by AKT1 E17K in Cancer / CD28 dependent PI3K/Akt signaling / Regulation of localization of FOXO transcription factors / positive regulation of glycogen biosynthetic process / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Activation of BAD and translocation to mitochondria / positive regulation of protein targeting to membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / regulation of cell migration / Regulation of TP53 Activity through Acetylation / FLT3 Signaling / Downregulation of ERBB2:ERBB3 signaling / VEGFR2 mediated vascular permeability / molecular function activator activity / protein localization to plasma membrane / Deactivation of the beta-catenin transactivating complex / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of glucose import / TP53 Regulates Metabolic Genes / protein modification process / ruffle membrane / Regulation of PTEN stability and activity / G beta:gamma signalling through PI3Kgamma / cellular response to insulin stimulus / glucose metabolic process / KEAP1-NFE2L2 pathway / Regulation of TP53 Degradation / insulin receptor signaling pathway / PIP3 activates AKT signaling / regulation of translation / cell cortex / early endosome / non-specific serine/threonine protein kinase / regulation of cell cycle / intracellular signal transduction / positive regulation of cell migration / phosphorylation / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barford, D. / Yang, J. / Hemmings, B.A. | ||||||
![]() | ![]() Title: Molecular Mechanism for the Regulation of Protein Kinase B/Akt by Hydrophobic Motif Phosphorylation Authors: Yang, J. / Cron, P. / Thompson, V. / Good, V. / Hess, D. / 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 | ![]() | 76.8 KB | Display | ![]() |
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PDB format | ![]() | 55.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424 KB | Display | ![]() |
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Full document | ![]() | 442.2 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 26.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gznC ![]() 1gzoC ![]() 1cdkS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36490.875 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES (146 - 460) 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: Water | ChemComp-HOH / |
-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: 10MG/ML PROTEIN, 30% PEG4K, 0.2 M LITHIUM SULPHATE, 0.1 M TRIS, pH 7.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||
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: Sep 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→35 Å / Num. obs: 113677 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21 |
Reflection | *PLUS Lowest resolution: 35 Å / Num. obs: 18905 / Num. measured all: 113677 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 77.8 % / Rmerge(I) obs: 0.243 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CDK Resolution: 2.3→34.98 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2389406.94 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 300 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→34.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PARAM19X.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 35 Å / % reflection Rfree: 7.1 % / Rfactor Rfree: 0.309 / Rfactor Rwork: 0.237 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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