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- PDB-7s6v: Leishmania infantum Glycogen Synthase Kinase 3 beta bound to CGP60474 -

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Basic information

Entry
Database: PDB / ID: 7s6v
TitleLeishmania infantum Glycogen Synthase Kinase 3 beta bound to CGP60474
ComponentsGlycogen synthase kinase 3
KeywordsTRANSFERASE/INHIBITOR / Protein kinase / inhibitor / TRANSFERASE / GSK3s / GSK3beta / Leishmania infantum / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


cell differentiation / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / signal transduction / ATP binding / nucleus / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-8II / Glycogen synthase kinase 3
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
Authorsdos Reis, C.V. / Ramos, P.Z. / Counago, R.M.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/50724-5 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)465651/2014-3 Brazil
Sao Paulo Research Foundation (FAPESP)2014/50897-0 Brazil
CitationJournal: To Be Published
Title: Leishmania infantum Glycogen Synthase Kinase 3 beta bound to CGP60474
Authors: Ramos, P.Z. / dos Reis, C.V. / Counago, R.M.
History
DepositionSep 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 20, 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

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Assembly

Deposited unit
A: Glycogen synthase kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4484
Polymers40,9341
Non-polymers5143
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-16 kcal/mol
Surface area15780 Å2
Unit cell
Length a, b, c (Å)156.163, 39.871, 62.801
Angle α, β, γ (deg.)90.000, 101.090, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glycogen synthase kinase 3


Mass: 40933.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: GSK3, LINF_180007700, LINJ_18_0270 / Production host: Escherichia coli (E. coli)
References: UniProt: A4HXQ3, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-8II / 3-({4-[2-(3-chloroanilino)pyrimidin-4-yl]pyridin-2-yl}amino)propan-1-ol


Mass: 355.821 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18ClN5O
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG3350 20%, 300 mM Li2SO4, 100 mM SBG (42.8 mM Sodium tartrate dihydrate, 28.6 mM Bis-Tris and 28.6 mM Glycylglycine)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 6, 2021
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.66→76.62 Å / Num. obs: 44340 / % possible obs: 98.6 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.025 / Rrim(I) all: 0.063 / Net I/σ(I): 15.8
Reflection shellResolution: 1.66→1.69 Å / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1896 / CC1/2: 0.695 / Rpim(I) all: 0.356 / Rrim(I) all: 0.873

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7S6U

7s6u


Resolution: 1.66→76.62 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.912 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 2120 4.8 %RANDOM
Rwork0.1839 ---
obs0.1854 42220 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.81 Å2 / Biso mean: 26.431 Å2 / Biso min: 13.49 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å2-0 Å2-0.58 Å2
2---1.16 Å2-0 Å2
3---0.35 Å2
Refinement stepCycle: final / Resolution: 1.66→76.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 34 209 2924
Biso mean--26.15 36.05 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132786
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172583
X-RAY DIFFRACTIONr_angle_refined_deg1.9351.6443784
X-RAY DIFFRACTIONr_angle_other_deg1.5421.5795928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1185345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55922.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0615447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5241517
X-RAY DIFFRACTIONr_chiral_restr0.1060.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02638
LS refinement shellResolution: 1.663→1.706 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 124 -
Rwork0.274 2836 -
all-2960 -
obs--90.69 %
Refinement TLS params.Method: refined / Origin x: 53.583 Å / Origin y: 23.206 Å / Origin z: 42.08 Å
111213212223313233
T0.0152 Å20.0201 Å20.0087 Å2-0.0289 Å20.0135 Å2--0.0423 Å2
L0.481 °20.1562 °2-0.0393 °2-0.2975 °20.0878 °2--0.3215 °2
S-0.0401 Å °-0.0782 Å °-0.0004 Å °0.0133 Å °0.0139 Å °0.101 Å °0.0525 Å °0.067 Å °0.0262 Å °

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