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Yorodumi- PDB-1uv5: GLYCOGEN SYNTHASE KINASE 3 BETA COMPLEXED WITH 6-BROMOINDIRUBIN-3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uv5 | ||||||
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Title | GLYCOGEN SYNTHASE KINASE 3 BETA COMPLEXED WITH 6-BROMOINDIRUBIN-3'-OXIME | ||||||
Components | GLYCOGEN SYNTHASE KINASE-3 BETA | ||||||
Keywords | TRANSFERASE / KINASE / INSULIN PATHWAY / WNT SIGNALING PATHWAY / TRANSFERASE SERINE/THREONINE-PROTEIN KINASE | ||||||
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: 2.8 Å | ||||||
Authors | Dajani, R. / Pearl, L.H. / Roe, S.M. | ||||||
Citation | Journal: Chem.Biol. / Year: 2003 Title: Gsk-3-Selective Inhibitors Derived from Tyrian Purple Indurubins Authors: Meijer, L. / Skaltsounis, A.-L. / Magiatis, P. / Polychronopoulous, P. / Knockaert, M. / Leost, M. / Ryan, X.P. / Vonica, C.A. / Brivanlou, A. / Dajani, R. / Crovace, C. / Tarricone, C. / ...Authors: Meijer, L. / Skaltsounis, A.-L. / Magiatis, P. / Polychronopoulous, P. / Knockaert, M. / Leost, M. / Ryan, X.P. / Vonica, C.A. / Brivanlou, A. / Dajani, R. / Crovace, C. / Tarricone, C. / Musacchio, A. / Roe, S.M. / Pearl, L.H. / Greengard, P. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uv5.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uv5.ent.gz | 65.4 KB | Display | PDB format |
PDBx/mmJSON format | 1uv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uv5_validation.pdf.gz | 724.6 KB | Display | wwPDB validaton report |
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Full document | 1uv5_full_validation.pdf.gz | 738.1 KB | Display | |
Data in XML | 1uv5_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 1uv5_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/1uv5 ftp://data.pdbj.org/pub/pdb/validation_reports/uv/1uv5 | HTTPS FTP |
-Related structure data
Related structure data | 1h8fS S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39658.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC HTA / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P49841, EC: 2.7.1.37 |
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-Non-polymers , 5 types, 117 molecules
#2: Chemical | ChemComp-BRW / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-CO / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | HIS 350 IN SWISS-PROT SHOULD BE LEU. THIS CONFLICT HAS BEEN DESCRIBED IN UNIPROT ENTRY P49841 |
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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: 5.1 Å3/Da / Density % sol: 75.6 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / 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: ID29 / Wavelength: 0.9253 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 7, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9253 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→35 Å / Num. obs: 24630 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 54.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 3.7 / % possible all: 99.7 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. obs: 50596 / Num. measured all: 220805 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 97 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 3.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H8F Resolution: 2.8→24.46 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1276631.37 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.413 Å2 / ksol: 0.350977 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→24.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.8 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.225 / Rfactor Rwork: 0.1925 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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