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- PDB-5v4x: Human glucokinase in complex with novel pyrazole activator. -

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Basic information

Entry
Database: PDB / ID: 5v4x
TitleHuman glucokinase in complex with novel pyrazole activator.
ComponentsGlucokinase
Keywordstransferase/transferase activator / activator / complex / glucokinase / transferase-transferase activator complex
Function / homology
Function and homology information


Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / mannokinase activity / glucose sensor activity / regulation of potassium ion transport / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose catabolic process / glucose 6-phosphate metabolic process ...Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / mannokinase activity / glucose sensor activity / regulation of potassium ion transport / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose catabolic process / glucose 6-phosphate metabolic process / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / NADP metabolic process / glucose binding / cellular response to leptin stimulus / calcium ion import / canonical glycolysis / Glycolysis / regulation of glycolytic process / intracellular glucose homeostasis / Regulation of gene expression in beta cells / regulation of insulin secretion / positive regulation of glycogen biosynthetic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / response to glucose / 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-8WJ / alpha-D-glucopyranose / IODIDE ION / Hexokinase-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.08 Å
AuthorsSkene, R.J. / Hosfiled, D.J.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: Discovery of potent and orally active 1,4-disubstituted indazoles as novel allosteric glucokinase activators.
Authors: Cheruvallath, Z.S. / Gwaltney, S.L. / Sabat, M. / Tang, M. / Wang, H. / Jennings, A. / Hosfield, D. / Lee, B. / Wu, Y. / Halkowycz, P. / Grimshaw, C.E.
History
DepositionMar 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4176
Polymers51,3931
Non-polymers1,0245
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.874, 77.855, 119.927
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 51392.527 Da / Num. of mol.: 1
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 / 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-8WJ / (2S)-3-cyclohexyl-2-[4-(cyclopentylsulfonyl)-2-oxopyridin-1(2H)-yl]-N-(1,3-thiazol-2-yl)propanamide


Mass: 463.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H29N3O4S2
#4: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 15% PEG3350, 200 mM ammonium iodide, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 26923 / % possible obs: 95.5 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.076 / Χ2: 1.03 / Net I/σ(I): 12.7 / Num. measured all: 151398
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
2.08-2.143.10.4430.916166.9
2.14-2.213.70.4360.979184.7
2.21-2.294.40.3011.02194.7
2.29-2.385.20.3091.017199
2.38-2.495.80.2341.062199.8
2.49-2.626.10.1921.1151100
2.62-2.786.20.141.0671100
2.78-36.40.0981.0721100
3-3.36.50.0751.0221100
3.3-3.786.40.0681.0171100
3.78-4.766.30.0580.9751100
4.76-506.10.0420.986199.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.08→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 11.151 / SU ML: 0.144 / SU R Cruickshank DPI: 0.2347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.201 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 1355 5 %RANDOM
Rwork0.1946 ---
obs0.1973 25508 95.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 115.97 Å2 / Biso mean: 42.197 Å2 / Biso min: 16.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å2-0 Å20 Å2
2--0.21 Å20 Å2
3----1.03 Å2
Refinement stepCycle: final / Resolution: 2.08→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 46 219 3546
Biso mean--45.75 45.48 -
Num. residues----420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193378
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9864541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7045416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.95323.806155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15515623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4051529
X-RAY DIFFRACTIONr_chiral_restr0.0960.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022494
LS refinement shellResolution: 2.082→2.136 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 77 -
Rwork0.293 1263 -
all-1340 -
obs--65.02 %
Refinement TLS params.Method: refined / Origin x: 19.4632 Å / Origin y: -7.212 Å / Origin z: -20.9418 Å
111213212223313233
T0.0262 Å2-0.0122 Å20.0072 Å2-0.0247 Å2-0.0001 Å2--0.0174 Å2
L0.8429 °20.0475 °20.7344 °2-0.7073 °20.3794 °2--1.5665 °2
S-0.0569 Å °0.0378 Å °0.0721 Å °-0.0207 Å °0.0041 Å °-0.0525 Å °-0.0097 Å °0.1126 Å °0.0528 Å °

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