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- PDB-2ow3: Glycogen synthase kinase-3 beta in complex with bis-(indole)malei... -

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Basic information

Entry
Database: PDB / ID: 2ow3
TitleGlycogen synthase kinase-3 beta in complex with bis-(indole)maleimide pyridinophane inhibitor
ComponentsGlycogen synthase kinase-3 beta
KeywordsTRANSFERASE / Kinase-inhibitor complex
Function / homology
Function and homology information


negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / 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 ...negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / 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 / regulation of microtubule-based process / CRMPs in Sema3A signaling / regulation of protein export from nucleus / heart valve development / 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 / regulation of axon extension / 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 / Maturation of nucleoprotein / AKT phosphorylates targets in the cytosol / positive regulation of cell-matrix adhesion / negative regulation of calcineurin-NFAT signaling cascade / dopamine receptor signaling pathway / regulation of dendrite morphogenesis / negative regulation of phosphoprotein phosphatase activity / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity / glycogen metabolic process / ER overload response / regulation of neuron projection development / Constitutive Signaling by AKT1 E17K in Cancer / dynactin binding / protein kinase A catalytic subunit binding / NF-kappaB binding / canonical Wnt signaling pathway / Regulation of HSF1-mediated heat shock response / epithelial to mesenchymal transition / negative regulation of osteoblast differentiation / negative regulation of protein-containing complex assembly / positive regulation of autophagy / regulation of microtubule cytoskeleton organization / regulation of cellular response to heat / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway in absence of ligand / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / positive regulation of protein export from nucleus / positive regulation of protein ubiquitination / Ubiquitin-dependent degradation of Cyclin D / hippocampus development / positive regulation of protein-containing complex assembly / 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 / negative regulation of canonical Wnt signaling pathway / tau protein binding / Degradation of beta-catenin by the destruction complex / B-WICH complex positively regulates rRNA expression / regulation of circadian rhythm / beta-catenin binding / positive regulation of GTPase activity / circadian rhythm / positive regulation of protein catabolic process / cellular response to amyloid-beta / neuron projection development / Regulation of RUNX2 expression and activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / presynapse / insulin receptor signaling pathway / positive regulation of protein binding / kinase activity / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation
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 / Protein kinase, ATP binding site ...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
BIS-(INDOLE)MALEIMIDE PYRIDINOPHANE / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhang, H.C. / Bonaga, L.V. / Ye, H. / Derian, C.K. / Damiano, B.P. / Maryanoff, B.E.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Novel bis(indolyl)maleimide pyridinophanes that are potent, selective inhibitors of glycogen synthase kinase-3.
Authors: Zhang, H.C. / Bonaga, L.V. / Ye, H. / Derian, C.K. / Damiano, B.P. / Maryanoff, B.E.
History
DepositionFeb 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)81,2514
Polymers80,1642
Non-polymers1,0872
Water27015
1
A: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6262
Polymers40,0821
Non-polymers5441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6262
Polymers40,0821
Non-polymers5441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.472, 117.329, 69.461
Angle α, β, γ (deg.)90.00, 103.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycogen synthase kinase-3 beta / / GSK-3 beta


Mass: 40081.980 Da / Num. of mol.: 2 / Fragment: residues 35-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSK3B / References: UniProt: P49841, tau-protein kinase
#2: Chemical ChemComp-BIM / BIS-(INDOLE)MALEIMIDE PYRIDINOPHANE


Mass: 543.658 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H33N5O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 3.44 Å3/Da / Density % sol: 64.2 %
Crystal growpH: 9 / Details: PEG2000, BICINE pH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 31, 2005 / Details: Dynamically blendable mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→67.6 Å / Num. all: 25427 / Num. obs: 25427 / % possible obs: 95.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 82.8 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 5.4
Reflection shellResolution: 2.8→3.02 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.0854 / Mean I/σ(I) obs: 1.3 / Num. unique all: 4465 / Rsym value: 0.0854 / % possible all: 79.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: previously derived model (originally from 1H8F)
Resolution: 2.8→67.57 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.862 / SU B: 16.974 / SU ML: 0.338 / Isotropic thermal model: isotrop / Cross valid method: THROUGHOUT / ESU R: 1.222 / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29483 1032 4.1 %RANDOM
Rwork0.24595 ---
all0.24794 25427 --
obs0.24794 25427 94.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.55 Å2
Baniso -1Baniso -2Baniso -3
1--2.31 Å20 Å2-0.94 Å2
2--6.45 Å20 Å2
3----4.57 Å2
Refine analyzeLuzzati coordinate error obs: 0.436 Å
Refinement stepCycle: LAST / Resolution: 2.8→67.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5584 0 82 15 5681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225745
X-RAY DIFFRACTIONr_bond_other_d0.0010.025265
X-RAY DIFFRACTIONr_angle_refined_deg1.0331.9987836
X-RAY DIFFRACTIONr_angle_other_deg0.742312232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4045686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.1723.04250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10215933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3581544
X-RAY DIFFRACTIONr_chiral_restr0.060.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026284
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021186
X-RAY DIFFRACTIONr_nbd_refined0.1880.21179
X-RAY DIFFRACTIONr_nbd_other0.1660.24981
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22778
X-RAY DIFFRACTIONr_nbtor_other0.0810.22986
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.269
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0750.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1680.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0610.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3224491
X-RAY DIFFRACTIONr_mcbond_other0.18421363
X-RAY DIFFRACTIONr_mcangle_it1.6735656
X-RAY DIFFRACTIONr_scbond_it2.14542732
X-RAY DIFFRACTIONr_scangle_it3.24562180
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 35 -
Rwork0.354 1277 -
obs-1277 66.13 %

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