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- PDB-4l3q: Crystal structure of glucokinase-activator complex -

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Basic information

Entry
Database: PDB / ID: 4l3q
TitleCrystal structure of glucokinase-activator complex
ComponentsGlucokinase
KeywordsTransferase/transferase activator / Glycolysis / Diabetes / Transferase-transferase activator complex
Function / homology
Function and homology information


Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / glucose sensor activity / regulation of potassium ion transport / mannokinase activity / hexokinase / glucose catabolic process / fructokinase activity / glucokinase activity / glucose 6-phosphate metabolic process / NADP+ metabolic process ...Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / glucose sensor activity / regulation of potassium ion transport / mannokinase activity / hexokinase / glucose catabolic process / fructokinase activity / glucokinase activity / glucose 6-phosphate metabolic process / NADP+ metabolic process / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / D-glucose binding / cellular response to leptin stimulus / canonical glycolysis / calcium ion import / Glycolysis / regulation of glycolytic process / intracellular glucose homeostasis / Regulation of gene expression in beta cells / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to glucose / regulation of insulin secretion / glycolytic process / positive regulation of insulin secretion / cellular response to insulin stimulus / glucose metabolic process / glucose homeostasis / mitochondrion / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. ...Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-926 / alpha-D-glucopyranose / Hexokinase-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsGajiwala, K.S. / Filipski, K.J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Pyrimidone-based series of glucokinase activators with alternative donor-acceptor motif.
Authors: Filipski, K.J. / Guzman-Perez, A. / Bian, J. / Perreault, C. / Aspnes, G.E. / Didiuk, M.T. / Dow, R.L. / Hank, R.F. / Jones, C.S. / Maguire, R.J. / Tu, M. / Zeng, D. / Liu, S. / Knafels, J.D. ...Authors: Filipski, K.J. / Guzman-Perez, A. / Bian, J. / Perreault, C. / Aspnes, G.E. / Didiuk, M.T. / Dow, R.L. / Hank, R.F. / Jones, C.S. / Maguire, R.J. / Tu, M. / Zeng, D. / Liu, S. / Knafels, J.D. / Litchfield, J. / Atkinson, K. / Derksen, D.R. / Bourbonais, F. / Gajiwala, K.S. / Hickey, M. / Johnson, T.O. / Humphries, P.S. / Pfefferkorn, J.A.
History
DepositionJun 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6273
Polymers51,1631
Non-polymers4642
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.512, 79.512, 321.131
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Glucokinase / Hexokinase type IV / HK IV / Hexokinase-4 / HK4 / Hexokinase-D


Mass: 51163.164 Da / Num. of mol.: 1 / Fragment: UNP residues 16-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GCK / Production host: Escherichia coli (E. coli) / References: UniProt: P35557, glucokinase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-926 / 6-{3-[(1-methyl-1H-imidazol-2-yl)sulfanyl]phenyl}pyridin-2(1H)-one


Mass: 283.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13N3OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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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: 2.86 Å3/Da / Density % sol: 57.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K / PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 2004 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 17490 / Num. obs: 17045 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.042 / Net I/σ(I): 32.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 9.3 / Num. unique all: 1678 / % possible all: 99.8

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Processing

Software
NameClassification
MAR345dtbdata collection
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1V4S

1v4s


Resolution: 2.7→39.84 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.866 / SU B: 14.604 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R: 1.089 / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30377 1769 10.1 %RANDOM
Rwork0.25415 ---
obs0.2591 15665 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.461 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.7→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3499 0 32 6 3537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213587
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9724823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8725446
X-RAY DIFFRACTIONr_chiral_restr0.1160.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022703
X-RAY DIFFRACTIONr_nbd_refined0.2370.21806
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2143
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2810.22
X-RAY DIFFRACTIONr_mcbond_it0.891.52205
X-RAY DIFFRACTIONr_mcangle_it1.68323537
X-RAY DIFFRACTIONr_scbond_it1.94631382
X-RAY DIFFRACTIONr_scangle_it3.4394.51286
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.428 133
Rwork0.339 1099

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