[English] 日本語
Yorodumi
- PDB-1q4l: GSK-3 Beta complexed with Inhibitor I-5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1q4l
TitleGSK-3 Beta complexed with Inhibitor I-5
ComponentsGLYCOGEN SYNTHASE KINASE-3 BETA
KeywordsTRANSFERASE / KINASE / INSULIN PATHWAY
Function / homology
Function and homology information


neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling / negative regulation of dopaminergic neuron differentiation ...neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling / 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 / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / CRMPs in Sema3A signaling / heart valve development / tau-protein kinase / 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 / regulation of long-term synaptic potentiation / negative regulation of TOR signaling / 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 / negative regulation of calcineurin-NFAT signaling cascade / Maturation of nucleoprotein / regulation of axon extension / negative regulation of epithelial to mesenchymal transition / G protein-coupled dopamine receptor signaling pathway / tau-protein kinase activity / positive regulation of cell-matrix adhesion / regulation of axonogenesis / regulation of dendrite morphogenesis / ER overload response / glycogen metabolic process / regulation of neuron projection development / establishment of cell polarity / protein kinase A catalytic subunit binding / Constitutive Signaling by AKT1 E17K in Cancer / dynactin binding / Regulation of HSF1-mediated heat shock response / negative regulation of osteoblast differentiation / epithelial to mesenchymal transition / canonical Wnt signaling pathway / NF-kappaB binding / negative regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of cellular response to heat / extrinsic apoptotic signaling pathway in absence of ligand / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / positive regulation of autophagy / presynaptic modulation of chemical synaptic transmission / Transcriptional and post-translational regulation of MITF-M expression and activity / regulation of microtubule cytoskeleton organization / response to endoplasmic reticulum stress / negative regulation of cell migration / hippocampus development / positive regulation of protein export from nucleus / positive regulation of protein ubiquitination / excitatory postsynaptic potential / mitochondrion organization / Ubiquitin-dependent degradation of Cyclin D / positive regulation of cell differentiation / positive regulation of protein-containing complex assembly / negative regulation of canonical Wnt signaling pathway / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / regulation of circadian rhythm / beta-catenin binding / Degradation of beta-catenin by the destruction complex / B-WICH complex positively regulates rRNA expression / tau protein binding / Wnt signaling pathway / circadian rhythm / cellular response to amyloid-beta / positive regulation of protein catabolic process / neuron projection development / Regulation of RUNX2 expression and activity / positive regulation of protein binding / kinase activity / p53 binding / positive regulation of neuron apoptotic process / insulin receptor signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / presynapse
Similarity search - Function
Glycogen synthase kinase 3, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-679 / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsBertrand, J.A. / Thieffine, S. / Vulpetti, A. / Cristiani, C. / Valsasina, B. / Knapp, S. / Kalisz, H.M. / Flocco, M.
CitationJournal: 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
DepositionAug 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLYCOGEN SYNTHASE KINASE-3 BETA
B: GLYCOGEN SYNTHASE KINASE-3 BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9174
Polymers94,1632
Non-polymers7542
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.167, 86.664, 178.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein GLYCOGEN SYNTHASE KINASE-3 BETA / GSK-3 BETA


Mass: 47081.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSK3B / Plasmid: PVL-GST-GSK3BETA / Cell line (production host): H5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P49841, EC: 2.7.1.37
#2: Chemical ChemComp-679 / 2-CHLORO-5-[4-(3-CHLORO-PHENYL)-2,5-DIOXO-2,5-DIHYDRO-1H-PYRROL-3-YLAMINO]-BENZOIC ACID / I-5


Mass: 377.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H10Cl2N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350 MONODISPERSE, GLYCEROL, MAGNESIUM CHLORIDE, HEPES, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112 mg/mlprotein1drop
210 %glycerol1drop
3185 mM1dropNaCl
4100 mMHEPES1droppH7.2
516-24 %(w/v)PEG3350 monodisperse1reservoir
65 %glycerol1reservoir
720 mM1reservoirMgCl2
8100 mMHEPES1reservoirpH7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 12, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.77→30 Å / Num. obs: 33530 / % possible obs: 98.5 % / Redundancy: 3.164 % / Biso Wilson estimate: 37.6 Å2 / Rsym value: 0.093 / Net I/σ(I): 10.8231
Reflection shellResolution: 2.77→2.87 Å / Mean I/σ(I) obs: 1.893 / Rsym value: 0.569 / % possible all: 99.6
Reflection
*PLUS
Highest resolution: 2.77 Å / Num. measured all: 106100 / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 1.9

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CNX2000refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H8F

1h8f


Resolution: 2.77→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1694956.14 / Data cutoff high rms absF: 1694956.14 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1660 5 %RANDOM
Rwork0.212 ---
obs-33497 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.3496 Å2 / ksol: 0.310392 e/Å3
Displacement parametersBiso mean: 53.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.08 Å20 Å20 Å2
2--15.22 Å20 Å2
3----18.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.77→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5418 0 50 47 5515
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d1.01
LS refinement shellResolution: 2.77→2.94 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 275 5 %
Rwork0.327 5273 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more