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- PDB-3fr0: Human glucokinase in complex with 2-amino benzamide activator -

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Basic information

Entry
Database: PDB / ID: 3fr0
TitleHuman glucokinase in complex with 2-amino benzamide activator
ComponentsGlucokinase
KeywordsTRANSFERASE / Hexokinase IV / Allosteric enzyme / Diabetes / Alternative splicing / ATP-binding / Diabetes mellitus / Disease mutation / Glycolysis / Kinase / Nucleotide-binding / Polymorphism
Function / homology
Function and homology information


Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / glucose sensor activity / mannokinase activity / regulation of potassium ion transport / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucose catabolic process / glucokinase activity / glucose 6-phosphate metabolic process ...Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / glucose sensor activity / mannokinase activity / regulation of potassium ion transport / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucose catabolic process / 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 / positive regulation of glycogen biosynthetic process / negative regulation of gluconeogenesis / 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-AJB / alpha-D-glucopyranose / Hexokinase-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKamata, K.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Identification of novel and potent 2-amino benzamide derivatives as allosteric glucokinase activators
Authors: Nishimura, T. / Iino, T. / Mitsuya, M. / Bamba, M. / Watanabe, H. / Tsukahara, D. / Kamata, K. / Sasaki, K. / Ohyama, S. / Hosaka, H. / Futamura, M. / Nagata, Y. / Eiki, J.
#1: Journal: Structure / Year: 2004
Title: Structural basis for allosteric regulation of the monomeric allosteric enzyme human glucokinase
Authors: Kamata, K. / Mitsuya, M. / Nishimura, T. / Eiki, J. / Nagata, Y.
History
DepositionJan 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 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 1.3Nov 1, 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5284
Polymers50,9791
Non-polymers5503
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.147, 80.147, 323.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 50978.902 Da / Num. of mol.: 1 / Fragment: Enzyme, UNP residues 12-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFLAG-CTC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alfa / 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-AJB / 2-amino-N-(4-methyl-1,3-thiazol-2-yl)-5-[(4-methyl-4H-1,2,4-triazol-3-yl)sulfanyl]benzamide / 2-amino-5-(4-methyl-4H-[1,2,4]triazole-3-yl-sulfanyl)-N-(4-methyl-thiazole-2-yl)benzamide


Mass: 346.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N6OS2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE FOR THIS PROTEIN IS BASED ON ISOFORM 2 OF HXK4_HUMAN (UNIPROTKB/SWISS-PROT P35557).

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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: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 30 % PEG 1500, HEPES, PH 6.6, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Oct 2, 2001 / Details: mirrors
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 17948 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Redundancy: 20.1 % / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 59.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 21.2 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 18.4 / Num. unique all: 2105 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNX2005phasing
CNX2005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V4S

1v4s


Resolution: 2.7→40.07 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 2281970 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.274 899 5 %RANDOM
Rwork0.211 ---
obs0.214 17830 99.6 %-
all-17830 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.639 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 106.69 Å2 / Biso mean: 44.146 Å2 / Biso min: 12.57 Å2
Baniso -1Baniso -2Baniso -3
1-4.71 Å26.09 Å20 Å2
2--4.71 Å20 Å2
3----9.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.7→40.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 36 134 3675
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.58
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.692
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_scangle_it3.562.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 142 4.9 %
Rwork0.274 2743 -
all-2885 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2GLC.parGLC.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5NIS.parNIS.top

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