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- PDB-7s6u: Leishmania infantum Glycogen Synthase Kinase 3 beta bound to AZD5438 -

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Basic information

Entry
Database: PDB / ID: 7s6u
TitleLeishmania infantum Glycogen Synthase Kinase 3 beta bound to AZD5438
ComponentsGlycogen synthase kinase 3GSK-3
KeywordsTRANSFERASE/INHIBITOR / Protein kinase / inhibitor / TRANSFERASE / GSK3s / GSK3beta / Leishmania infantum / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / protein phosphorylation / protein serine/threonine kinase activity / ATP binding
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
CACODYLATE ION / Chem-FB8 / Glycogen synthase kinase 3
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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 AZD5438
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

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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)41,6296
Polymers40,9341
Non-polymers6955
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint10 kcal/mol
Surface area16060 Å2
Unit cell
Length a, b, c (Å)156.368, 39.519, 62.608
Angle α, β, γ (deg.)90.000, 100.530, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glycogen synthase kinase 3 / GSK-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-FB8 / 4-(2-methyl-3-propan-2-yl-imidazol-4-yl)-~{N}-(4-methylsulfonylphenyl)pyrimidin-2-amine


Mass: 371.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21N5O2S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG 3350, 0.2 M Sodium bromide, 10% Ethylene glycol, 0.1 M SSB (0.04 M Sodium propionate, 0.02 M Sodium cacodylate trihydrate and 0.04 M Bis-Tris propane)

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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: Oct 22, 2020
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: 1.74→29.26 Å / Num. obs: 38529 / % possible obs: 98.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 26.983 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.033 / Rrim(I) all: 0.075 / Net I/σ(I): 11.4
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.051 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2106 / CC1/2: 0.514 / Rpim(I) all: 0.51 / Rrim(I) all: 1.173 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E3P

3e3p


Resolution: 1.74→29.26 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.035 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2001 1870 4.9 %RANDOM
Rwork0.1732 ---
obs0.1746 36651 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.4 Å2 / Biso mean: 32.377 Å2 / Biso min: 18.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-0.2 Å2
2--0.08 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 1.74→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 43 179 2949
Biso mean--39.13 41.7 -
Num. residues----351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132837
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172638
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.6493853
X-RAY DIFFRACTIONr_angle_other_deg1.5291.5796049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6495351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72422.042142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58215452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2261519
X-RAY DIFFRACTIONr_chiral_restr0.1020.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023211
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02648
LS refinement shellResolution: 1.74→1.785 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 131 -
Rwork0.264 2716 -
all-2847 -
obs--98.96 %
Refinement TLS params.Method: refined / Origin x: 53.8061 Å / Origin y: 22.9359 Å / Origin z: 42.2632 Å
111213212223313233
T0.0342 Å20.0319 Å2-0.011 Å2-0.0317 Å20.0023 Å2--0.0857 Å2
L0.4027 °20.1701 °20.0264 °2-0.159 °20.177 °2--0.3556 °2
S-0.0643 Å °-0.0602 Å °0.0575 Å °0.0095 Å °0.0152 Å °0.072 Å °0.0836 Å °0.0857 Å °0.0491 Å °

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