+Open data
-Basic information
Entry | Database: PDB / ID: 1pyx | ||||||
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Title | GSK-3 Beta complexed with AMP-PNP | ||||||
Components | Glycogen synthase kinase-3 beta | ||||||
Keywords | TRANSFERASE / KINASE / INSULIN PATHWAY | ||||||
Function / homology | Function and homology information regulation of microtubule anchoring at centrosome / negative regulation of glycogen (starch) synthase activity / neuron projection organization / beta-catenin destruction complex disassembly / negative regulation of mesenchymal stem cell differentiation / 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 ...regulation of microtubule anchoring at centrosome / negative regulation of glycogen (starch) synthase activity / neuron projection organization / beta-catenin destruction complex disassembly / negative regulation of mesenchymal stem cell differentiation / 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 / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of protein localization to centrosome / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of cilium assembly / 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 / 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 / Maturation of nucleoprotein / cellular response to interleukin-3 / Wnt signalosome / negative regulation of TOR signaling / negative regulation of protein localization to nucleus / Disassembly of the destruction complex and recruitment of AXIN to the membrane / regulation of long-term synaptic potentiation / 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 / establishment of cell polarity / tau-protein kinase activity / negative regulation of osteoblast differentiation / regulation of axonogenesis / regulation of dendrite morphogenesis / glycogen metabolic process / ER overload response / regulation of neuron projection development / Constitutive Signaling by AKT1 E17K in Cancer / protein kinase A catalytic subunit binding / dynactin binding / NF-kappaB binding / Transcriptional and post-translational regulation of MITF-M expression and activity / Regulation of HSF1-mediated heat shock response / canonical Wnt signaling pathway / epithelial to mesenchymal transition / negative regulation of protein-containing complex assembly / positive regulation of autophagy / regulation of microtubule cytoskeleton organization / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of cellular response to heat / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / presynaptic modulation of chemical synaptic transmission / excitatory postsynaptic potential / positive regulation of protein export from nucleus / positive regulation of GTPase activity / negative regulation of cell migration / mitochondrion organization / positive regulation of protein ubiquitination / Ubiquitin-dependent degradation of Cyclin D / regulation of circadian rhythm / hippocampus development / positive regulation of cell differentiation / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / peptidyl-threonine phosphorylation / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / positive regulation of protein-containing complex assembly / B-WICH complex positively regulates rRNA expression / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / circadian rhythm / tau protein binding / p53 binding / beta-catenin binding / positive regulation of protein catabolic process / cellular response to amyloid-beta / Regulation of RUNX2 expression and activity / neuron projection development / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of protein binding / insulin receptor signaling pathway / presynapse / kinase activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Bertrand, J.A. / Thieffine, S. / Vulpetti, A. / Cristiani, C. / Valsasina, B. / Knapp, S. / Kalisz, H.M. / Flocco, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Structural characterization of the GSK-3beta active site using selective and non-selective ATP-mimetic inhibitors Authors: Bertrand, J.A. / Thieffine, S. / Vulpetti, A. / Cristiani, C. / Valsasina, B. / Knapp, S. / Kalisz, H.M. / Flocco, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pyx.cif.gz | 155.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pyx.ent.gz | 119.6 KB | Display | PDB format |
PDBx/mmJSON format | 1pyx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pyx_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1pyx_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1pyx_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 1pyx_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/1pyx ftp://data.pdbj.org/pub/pdb/validation_reports/py/1pyx | HTTPS FTP |
-Related structure data
Related structure data | 1q3dC 1q3wC 1q41C 1q4lC 1h8fS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46955.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSK3B / Cell line (production host): H5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P49841, EC: 2.7.1.37 #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.16 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / pH: 7 Details: PEG 3350 monodisperse, Glycerol, Magnesium Chloride, Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.00 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→19.9 Å / Num. obs: 49993 / % possible obs: 98.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 32.8 Å2 / Rsym value: 0.076 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.4→2.49 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.518 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.4 Å / Num. obs: 50028 / Num. measured all: 206766 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H8F Resolution: 2.4→19.92 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2029928.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.1199 Å2 / ksol: 0.407602 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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