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- PDB-5kpk: Glycogen Synthase Kinase 3 beta Complexed with BRD0209 -

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Basic information

Entry
Database: PDB / ID: 5kpk
TitleGlycogen Synthase Kinase 3 beta Complexed with BRD0209
ComponentsGlycogen synthase kinase-3 beta
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


regulation of microtubule anchoring at centrosome / beta-catenin destruction complex disassembly / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / neuron projection organization / 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 / beta-catenin destruction complex disassembly / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / neuron projection organization / 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 / positive regulation of protein localization to centrosome / maintenance of cell polarity / 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 / negative regulation of TOR signaling / Wnt signalosome / regulation of long-term synaptic potentiation / negative regulation of protein localization to nucleus / Disassembly of the destruction complex and recruitment of AXIN to the membrane / AKT phosphorylates targets in the cytosol / Maturation of nucleoprotein / negative regulation of epithelial to mesenchymal transition / 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 axonogenesis / regulation of dendrite morphogenesis / tau-protein kinase activity / establishment of cell polarity / 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 / Regulation of HSF1-mediated heat shock response / negative regulation of osteoblast differentiation / epithelial to mesenchymal transition / negative regulation of protein-containing complex assembly / canonical Wnt signaling pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / 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 in absence of ligand / extrinsic apoptotic signaling pathway / presynaptic modulation of chemical synaptic transmission / positive regulation of GTPase activity / positive regulation of protein export from nucleus / excitatory postsynaptic potential / negative regulation of cell migration / positive regulation of protein ubiquitination / mitochondrion organization / Ubiquitin-dependent degradation of Cyclin D / hippocampus development / positive regulation of cell differentiation / peptidyl-threonine phosphorylation / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / positive regulation of protein-containing complex assembly / negative regulation of canonical Wnt signaling pathway / tau protein binding / B-WICH complex positively regulates rRNA expression / Degradation of beta-catenin by the destruction complex / regulation of circadian rhythm / beta-catenin binding / circadian rhythm / positive regulation of protein catabolic process / cellular response to amyloid-beta / Regulation of RUNX2 expression and activity / neuron projection development / p53 binding / positive regulation of protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / insulin receptor signaling pathway / kinase activity
Similarity search - Function
Glycogen synthase kinase 3, catalytic domain / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Glycogen synthase kinase 3, catalytic domain / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-6VK / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLakshminarasimhan, D. / White, A. / Nadupalli, A. / Suto, R.K.
CitationJournal: Sci Transl Med / Year: 2018
Title: Exploiting an Asp-Glu "switch" in glycogen synthase kinase 3 to design paralog-selective inhibitors for use in acute myeloid leukemia.
Authors: Wagner, F.F. / Benajiba, L. / Campbell, A.J. / Weiwer, M. / Sacher, J.R. / Gale, J.P. / Ross, L. / Puissant, A. / Alexe, G. / Conway, A. / Back, M. / Pikman, Y. / Galinsky, I. / DeAngelo, D. ...Authors: Wagner, F.F. / Benajiba, L. / Campbell, A.J. / Weiwer, M. / Sacher, J.R. / Gale, J.P. / Ross, L. / Puissant, A. / Alexe, G. / Conway, A. / Back, M. / Pikman, Y. / Galinsky, I. / DeAngelo, D.J. / Stone, R.M. / Kaya, T. / Shi, X. / Robers, M.B. / Machleidt, T. / Wilkinson, J. / Hermine, O. / Kung, A. / Stein, A.J. / Lakshminarasimhan, D. / Hemann, M.T. / Scolnick, E. / Zhang, Y.L. / Pan, J.Q. / Stegmaier, K. / Holson, E.B.
History
DepositionJul 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogen synthase kinase-3 beta
B: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0544
Polymers94,3592
Non-polymers6952
Water4,324240
1
A: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5272
Polymers47,1791
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5272
Polymers47,1791
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.367, 67.709, 67.558
Angle α, β, γ (deg.)79.560, 88.180, 76.500
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Glycogen synthase kinase-3 beta / GSK-3 beta / Serine/threonine-protein kinase GSK3B


Mass: 47179.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSK3B / Plasmid: PACg2T Baculogold / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: P49841, tau-protein kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-6VK / (4~{S})-3-cyclopropyl-4,7,7-trimethyl-4-phenyl-2,6,8,9-tetrahydropyrazolo[3,4-b]quinolin-5-one


Mass: 347.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25N3O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Reservoir: 0.15 M DL-malic acid, pH 7.0, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 41861 / % possible obs: 98 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.071 / Χ2: 0.987 / Net I/av σ(I): 17.433 / Net I/σ(I): 9.8 / Num. measured all: 156205
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.493.40.506194.4
2.49-2.593.60.412197.4
2.59-2.73.80.317197.9
2.7-2.853.80.241198
2.85-3.023.80.163198.2
3.02-3.263.80.119198.5
3.26-3.583.80.079198.7
3.58-4.13.80.06198.9
4.1-5.173.70.049199.3
5.17-503.70.038199.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.849 / SU ML: 0.176 / SU R Cruickshank DPI: 0.2447 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.211 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 2099 5 %RANDOM
Rwork0.167 ---
obs0.1699 39762 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 153.63 Å2 / Biso mean: 55.822 Å2 / Biso min: 28.22 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20.72 Å22.58 Å2
2---0.47 Å2-0.13 Å2
3----1.06 Å2
Refinement stepCycle: final / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5544 0 52 240 5836
Biso mean--38.05 52.39 -
Num. residues----692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195744
X-RAY DIFFRACTIONr_bond_other_d0.0020.025515
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.9967836
X-RAY DIFFRACTIONr_angle_other_deg1.106312688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2885688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45722.988251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.53415943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2821546
X-RAY DIFFRACTIONr_chiral_restr0.110.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216378
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021316
X-RAY DIFFRACTIONr_mcbond_it4.6175.342764
X-RAY DIFFRACTIONr_mcbond_other4.6165.3392765
X-RAY DIFFRACTIONr_mcangle_it6.8517.9933448
LS refinement shellResolution: 2.395→2.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 132 -
Rwork0.296 2609 -
all-2741 -
obs--86.77 %

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