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- PDB-7sxf: BIO-2895 (BRD0705) bound GSK3alpha-axin complex -

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Basic information

Entry
Database: PDB / ID: 7sxf
TitleBIO-2895 (BRD0705) bound GSK3alpha-axin complex
Components
  • Axin peptide
  • Glycogen synthase kinase-3 alpha
KeywordsHYDROLASE / kinase
Function / homology
Function and homology information


negative regulation of UDP-glucose catabolic process / positive regulation of heart contraction / cardiac left ventricle morphogenesis / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / regulation of mitophagy / negative regulation of glycogen biosynthetic process / negative regulation of cell growth involved in cardiac muscle cell development / negative regulation of D-glucose import / regulation of systemic arterial blood pressure ...negative regulation of UDP-glucose catabolic process / positive regulation of heart contraction / cardiac left ventricle morphogenesis / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / regulation of mitophagy / negative regulation of glycogen biosynthetic process / negative regulation of cell growth involved in cardiac muscle cell development / negative regulation of D-glucose import / regulation of systemic arterial blood pressure / XBP1(S) activates chaperone genes / autosome genomic imprinting / Suppression of apoptosis / proximal dendrite / beta-catenin destruction complex / tau-protein kinase / apical dendrite / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / Maturation of nucleoprotein / cellular response to interleukin-3 / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / negative regulation of TOR signaling / AKT phosphorylates targets in the cytosol / positive regulation of protein targeting to mitochondrion / Maturation of nucleoprotein / tau-protein kinase activity / G protein-coupled dopamine receptor signaling pathway / positive regulation of amyloid-beta formation / cellular response to glucocorticoid stimulus / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / cellular response to lithium ion / glycogen metabolic process / regulation of neuron projection development / Constitutive Signaling by AKT1 E17K in Cancer / protein kinase A catalytic subunit binding / extrinsic apoptotic signaling pathway / positive regulation of protein ubiquitination / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of autophagy / negative regulation of insulin receptor signaling pathway / regulation of microtubule cytoskeleton organization / excitatory postsynaptic potential / negative regulation of canonical Wnt signaling pathway / tau protein binding / Wnt signaling pathway / cellular response to insulin stimulus / positive regulation of protein catabolic process / insulin receptor signaling pathway / cell migration / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nervous system development / positive regulation of neuron apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / non-specific serine/threonine protein kinase / postsynapse / viral protein processing / axon / signaling receptor binding / protein serine kinase activity / neuronal cell body / protein serine/threonine kinase activity / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Glycogen synthase kinase 3, catalytic domain / : / 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
Similarity search - Domain/homology
Chem-6VL / Glycogen synthase kinase-3 alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsChodaparambil, J.V.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Acs Chem Neurosci / Year: 2023
Title: Elucidation of the GSK3 alpha Structure Informs the Design of Novel, Paralog-Selective Inhibitors.
Authors: Amaral, B. / Capacci, A. / Anderson, T. / Tezer, C. / Bajrami, B. / Lulla, M. / Lucas, B. / Chodaparambil, J.V. / Marcotte, D. / Kumar, P.R. / Murugan, P. / Spilker, K. / Cullivan, M. / ...Authors: Amaral, B. / Capacci, A. / Anderson, T. / Tezer, C. / Bajrami, B. / Lulla, M. / Lucas, B. / Chodaparambil, J.V. / Marcotte, D. / Kumar, P.R. / Murugan, P. / Spilker, K. / Cullivan, M. / Wang, T. / Peterson, A.C. / Enyedy, I. / Ma, B. / Chen, T. / Yousaf, Z. / Calhoun, M. / Golonzhka, O. / Dillon, G.M. / Koirala, S.
History
DepositionNov 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycogen synthase kinase-3 alpha
B: Axin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6634
Polymers41,3022
Non-polymers3612
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-24 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.930, 55.710, 66.560
Angle α, β, γ (deg.)90.000, 97.711, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Glycogen synthase kinase-3 alpha / GSK-3 alpha / Serine/threonine-protein kinase GSK3A


Mass: 39292.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSK3A / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P49840, tau-protein kinase, non-specific serine/threonine protein kinase
#2: Protein/peptide Axin peptide


Mass: 2009.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-6VL / (4~{S})-4-ethyl-7,7-dimethyl-4-phenyl-2,6,8,9-tetrahydropyrazolo[3,4-b]quinolin-5-one


Mass: 321.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M calcium acetate, 0.1M BisTRIS pH 7.0, 5% Glycerol and 17% PEG3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.94→47.43 Å / Num. obs: 31698 / % possible obs: 97.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 47.64 Å2 / CC1/2: 0.99 / Net I/σ(I): 24.4
Reflection shellResolution: 1.94→2.01 Å / Rmerge(I) obs: 0.14 / Num. unique obs: 11370 / CC1/2: 0.98

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5kpm

5kpm


Resolution: 1.94→47.43 Å / SU ML: 0.3011 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7512
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2347 1996 6.3 %
Rwork0.2011 29702 -
obs0.2032 31698 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.37 Å2
Refinement stepCycle: LAST / Resolution: 1.94→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 25 101 2893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612902
X-RAY DIFFRACTIONf_angle_d0.88123969
X-RAY DIFFRACTIONf_chiral_restr0.0518454
X-RAY DIFFRACTIONf_plane_restr0.0106511
X-RAY DIFFRACTIONf_dihedral_angle_d6.0507422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.48021210.50311812X-RAY DIFFRACTION84.34
1.99-2.040.37371430.39422114X-RAY DIFFRACTION98.56
2.04-2.10.34061420.29912120X-RAY DIFFRACTION98.31
2.1-2.170.26871430.262125X-RAY DIFFRACTION98.1
2.17-2.250.27011430.24422114X-RAY DIFFRACTION98.13
2.25-2.340.28011440.2372131X-RAY DIFFRACTION98.14
2.34-2.440.30271440.25472151X-RAY DIFFRACTION98.33
2.44-2.570.27681420.22512125X-RAY DIFFRACTION98.31
2.57-2.730.23261440.20972142X-RAY DIFFRACTION99.13
2.73-2.940.26471460.20242158X-RAY DIFFRACTION98.88
2.94-3.240.23971450.21462160X-RAY DIFFRACTION99.31
3.24-3.710.23421450.18652177X-RAY DIFFRACTION98.89
3.71-4.670.19041460.16022159X-RAY DIFFRACTION98.59
4.67-47.430.20641480.18572214X-RAY DIFFRACTION98.38
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.091194049671.57337971965-0.24964922993.2116873061.686095245633.96699282184-0.8530759305911.38402964071-0.545929065285-1.00160352210.357858577292-0.8780291323730.4774037531781.195588872990.4153696768250.744593686241-0.02390576857880.4250499611641.665479514930.2270567861711.087123855314.18823287374-16.557024459110.4280305883
24.955057823590.01130052342.647772167218.74758170143-5.055692894044.70274087417-0.7424349799081.085958407840.5548083884290.01220756673410.7072083974570.177344328352-0.845636014453-0.2169928106150.07221455100680.614987649332-0.04411128454590.1048167646980.7740233699420.348478541850.737588230078-8.32708316803-8.4386307829315.6399408055
32.62352318922-0.1067202030711.400993736580.8860838825490.2948082470722.22514833721-0.2443911182570.6897867581880.411886826174-0.4261873737640.141428815031-0.294064349123-0.3535532688360.4139729644090.07845467234320.472563568320.002819521857880.07139289290510.6453554818960.0922118768260.478024964489-11.0652798498-17.610153857217.4687868905
42.986176279130.318520956883-0.5609913498722.51056116220.5390848292514.9299603323-0.03899849516210.514039146355-0.143565914569-0.317735224343-0.08353328780810.0708601961460.38396629143-0.03104706447360.1592455864160.3805675766870.0281624861801-0.01941831880450.282607923437-0.03716044554760.325381494762-27.3426744866-29.343091319721.7646364014
54.53782307355-0.885434403212-1.679970613063.2605092198-1.283986437293.275628238840.214559260321-0.1352697264531.070304211690.7113611574850.122017868349-0.142498230293-1.162531648940.573240752106-0.3167417711430.886336206823-0.2095418362440.3194429971780.553694470465-0.2837807555190.812124674569-35.9652589953-20.74734545744.6948256661
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 101 through 118 )AA101 - 1181 - 18
22chain 'A' and (resid 119 through 151 )AA119 - 15119 - 48
33chain 'A' and (resid 152 through 217 )AA152 - 21749 - 112
44chain 'A' and (resid 218 through 445 )AA218 - 445113 - 340
55chain 'B' and (resid 383 through 399 )BB383 - 3991 - 17

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