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- PDB-3zdi: Glycogen Synthase Kinase 3 Beta complexed with Axin Peptide and I... -

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Basic information

Entry
Database: PDB / ID: 3zdi
TitleGlycogen Synthase Kinase 3 Beta complexed with Axin Peptide and Inhibitor 7d
Components
  • AXIN-1AXIN1
  • GLYCOGEN SYNTHASE KINASE-3 BETA
KeywordsTRANSFERASE/PEPTIDE / TRANSFERASE-PEPTIDE COMPLEX / INSULIN PATHWAY / WNT SIGNALING PATHWAY / TRANSFERASE SERINE/THREONINE-PROTEIN KINASE / INHIBITOR
Function / homology
Function and homology information


armadillo repeat domain binding / head development / cell development / negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / beta-catenin destruction complex disassembly / negative regulation of mesenchymal stem cell differentiation / dorsal/ventral axis specification / negative regulation of type B pancreatic cell development ...armadillo repeat domain binding / head development / cell development / negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / beta-catenin destruction complex disassembly / negative regulation of mesenchymal stem cell differentiation / dorsal/ventral axis specification / negative regulation of type B pancreatic cell development / axial mesoderm formation / 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 / post-anal tail morphogenesis / 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 / epigenetic programming in the zygotic pronuclei / beta-catenin destruction complex / tau-protein kinase / positive regulation of ubiquitin-dependent protein catabolic process / CRMPs in Sema3A signaling / regulation of microtubule-based process / heart valve development / 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 / I-SMAD binding / cellular response to interleukin-3 / Wnt signalosome / negative regulation of protein localization to nucleus / regulation of long-term synaptic potentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Maturation of nucleoprotein / AKT phosphorylates targets in the cytosol / nucleocytoplasmic transport / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of protein metabolic process / positive regulation of cell-matrix adhesion / regulation of axon extension / dopamine receptor signaling pathway / negative regulation of fat cell differentiation / negative regulation of phosphoprotein phosphatase activity / regulation of dendrite morphogenesis / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity / glycogen metabolic process / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / ER overload response / regulation of neuron projection development / negative regulation of transcription elongation by RNA polymerase II / positive regulation of transforming growth factor beta receptor signaling pathway / activation of protein kinase activity / Constitutive Signaling by AKT1 E17K in Cancer / SMAD binding / protein kinase A catalytic subunit binding / dynactin binding / R-SMAD binding / ubiquitin-like ligase-substrate adaptor activity / NF-kappaB binding / lateral plasma membrane / 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 / signaling adaptor activity / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / regulation of cellular response to heat / cellular response to retinoic acid / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway / 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 peptidyl-threonine phosphorylation / positive regulation of protein ubiquitination / TCF dependent signaling in response to WNT / Ubiquitin-dependent degradation of Cyclin D / cell periphery / hippocampus development / positive regulation of cell differentiation
Similarity search - Function
Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin ...Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / RGS, subdomain 1/3 / Glycogen synthase kinase 3, catalytic domain / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Ubiquitin-like domain superfamily / 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
PHOSPHATE ION / Chem-UGJ / Axin-1 / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.645 Å
AuthorsOberholzer, A.E. / Pearl, L.H.
CitationJournal: J.Med.Chem. / Year: 2013
Title: 3,6-Diamino-4-(2-Halophenyl)-2-Benzoylthieno(2,3-B) Pyridine-5-Carbonitriles are Selective Inhibitors of Plasmodium Falciparum Glycogen Synthase Kinase-3 (Pfgsk-3)
Authors: Fugel, W. / Oberholzer, A.E. / Gschloessl, B. / Dzikowski, R. / Pressburger, N. / Preu, L. / Pearl, L.H. / Baratte, B. / Ratin, M. / Okun, I. / Doerig, C. / Kruggel, S. / Lemcke, T. / Meijer, L. / Kunick, C.
History
DepositionNov 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCOGEN SYNTHASE KINASE-3 BETA
B: AXIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4434
Polymers42,0222
Non-polymers4212
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-20.2 kcal/mol
Surface area17710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.147, 76.157, 86.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLYCOGEN SYNTHASE KINASE-3 BETA / / GSK-3 BETA / SERINE/THREONINE-PROTEIN KINASE GSK3B


Mass: 39882.773 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-384
Source method: isolated from a genetically manipulated source
Details: PHOSPHOTYROSINE AT A216 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P49841, tau-protein kinase, non-specific serine/threonine protein kinase
#2: Protein/peptide AXIN-1 / AXIN1 / AXIS INHIBITION PROTEIN 1 / HAXIN


Mass: 2139.428 Da / Num. of mol.: 1 / Fragment: RESIDUES 383-400 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O15169
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-UGJ / 3,6-Diamino-4-(2-chlorophenyl)thieno[2,3-b]pyridine-2,5-dicarbonitrile


Mass: 325.776 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H8ClN5S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.12 % / Description: NONE
Crystal growDetails: 0.1 M 2-(N-MORPHOLINO)ETHANESULFONIC ACID (MES), PH 6.5, 12% (W/V) PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.64→45.05 Å / Num. obs: 14488 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 58.41 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18
Reflection shellResolution: 2.64→2.8 Å / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.3 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O9U

1o9u


Resolution: 2.645→45.046 Å / SU ML: 0.35 / σ(F): 2 / Phase error: 24.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2423 869 6 %
Rwork0.2011 --
obs0.2036 14481 98.77 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.28 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-18.4992 Å20 Å20 Å2
2---1.334 Å20 Å2
3----17.1653 Å2
Refinement stepCycle: LAST / Resolution: 2.645→45.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 27 70 3029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033033
X-RAY DIFFRACTIONf_angle_d0.754132
X-RAY DIFFRACTIONf_dihedral_angle_d12.7841134
X-RAY DIFFRACTIONf_chiral_restr0.057459
X-RAY DIFFRACTIONf_plane_restr0.004531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6449-2.81060.32971390.2952186X-RAY DIFFRACTION97
2.8106-3.02760.34681430.27662245X-RAY DIFFRACTION100
3.0276-3.33220.28281460.23442274X-RAY DIFFRACTION100
3.3322-3.81410.23391440.19862267X-RAY DIFFRACTION100
3.8141-4.80450.19321470.16562293X-RAY DIFFRACTION100
4.8045-45.05220.23681500.18542347X-RAY DIFFRACTION97
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)
12.924-0.95390.30886.2532-1.47316.26370.18670.11650.2134-0.3354-0.0966-0.6988-0.90850.8507-0.17930.3481-0.0910.04620.48530.02130.3786-10.47554.0299-0.5009
21.79760.22350.16271.5953-0.37792.57230.16410.24180.0606-0.1196-0.2533-0.10140.03910.0880.10120.62120.01460.02610.52090.03650.4166-11.5695-4.0539-4.091
30.15080.65020.46255.4326-0.75764.05570.16620.0720.3631-0.0927-0.062-0.1046-0.53950.7744-0.02390.3017-0.0795-0.11170.58410.04360.3642-13.3069-2.3309-2.2068
42.23050.5054-1.53283.6625-1.47193.4857-0.0175-0.19370.04880.0523-0.1938-0.10410.18020.22880.21450.18490.03380.00260.32730.00620.3095-16.7948-10.486514.2358
53.7454-1.345-1.00485.41-0.3692.5856-0.10540.062-0.6639-0.3129-0.09020.68931.84070.45870.16390.96410.1280.12810.519-0.1140.6872-12.5583-22.1205-0.3545
61.711-0.8266-0.69870.7433-0.23881.2459-0.460.0604-0.7549-0.4194-0.3452-0.62961.94321.11930.32110.76430.38780.20410.4970.16140.6206-11.0381-27.563914.1273
70.1946-0.02410.030.0893-0.4111.9911-0.259-0.129-0.74290.40190.1827-0.54381.58910.4038-0.24711.69790.42070.4720.310.01741.1989-13.1017-42.765611.8056
85.091-1.1845-0.83185.48-1.39095.1347-0.358-0.449-0.73570.05360.07680.13531.09880.00360.22950.5208-0.06440.0820.37310.08980.4452-24.7763-25.418420.5827
93.83491.54741.64325.22371.76156.4533-0.2052-0.02750.39660.0160.26960.6314-0.447-0.7095-0.05160.47280.0396-0.00370.49780.09410.4487-35.4285-11.007614.8839
100.6782-0.380.32480.986-0.450.8737-0.1617-0.2269-0.4345-0.00370.2258-0.39940.63330.18740.17171.94420.67150.33430.65220.18931.4416-0.8918-41.719112.6298
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 36:74)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 75:103)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 104:125)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 126:198)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 199:219)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 220:273)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 274:300)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 301:344)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 345:384)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 422:438)

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