+Open data
-Basic information
Entry | Database: PDB / ID: 1mry | ||||||
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Title | crystal structure of an inactive akt2 kinase domain | ||||||
Components | RAC-beta serine/threonine kinase | ||||||
Keywords | TRANSFERASE / AGC serine threonine kinase / AKT PKB kinase domain / tumorigenesis / x-ray crystal structure / signal transduction | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Huang, X. / Begley, M. / Morgenstern, K.A. / Gu, Y. / Rose, P. / Zhao, H. / Zhu, X. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Crystal structure of an inactive akt2 kinase domain Authors: Huang, X. / Begley, M. / Morgenstern, K.A. / Gu, Y. / Rose, P. / Zhao, H. / Zhu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mry.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mry.ent.gz | 49.2 KB | Display | PDB format |
PDBx/mmJSON format | 1mry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mry_validation.pdf.gz | 366.4 KB | Display | wwPDB validaton report |
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Full document | 1mry_full_validation.pdf.gz | 374.2 KB | Display | |
Data in XML | 1mry_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 1mry_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/1mry ftp://data.pdbj.org/pub/pdb/validation_reports/mr/1mry | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 39313.008 Da / Num. of mol.: 1 / Fragment: kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKT2 Plasmid details: gene cloned between BamHI & EcoRI, has His6 tag with thrombin cleavage site. Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P31751, non-specific serine/threonine protein kinase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.01 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Li2SO4, PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 170 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→100 Å / Num. obs: 17737 / Redundancy: 4.46 % / Biso Wilson estimate: 51.46 Å2 / Rmerge(I) obs: 0.059 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. obs: 11332 / % possible obs: 98.3 % / Num. measured all: 63147 / Rmerge(I) obs: 0.055 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PKA in ternary complex Resolution: 2.8→100 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→100 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.8 Å / Rfactor Rfree: 0.277 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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