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- PDB-3h1v: Human glucokinase in complex with a synthetic activator -

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Basic information

Entry
Database: PDB / ID: 3h1v
TitleHuman glucokinase in complex with a synthetic activator
ComponentsGlucokinase
KeywordsTRANSFERASE / glucokinase / diabetes / allosteric activator / 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) / cellular response to leptin stimulus / D-glucose binding / 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
alpha-D-glucopyranose / Chem-TK1 / Hexokinase-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.11 Å
AuthorsKamata, K. / Takahashi, K.
CitationJournal: Bioorg.Med.Chem. / Year: 2009
Title: The design and optimization of a series of 2-(pyridin-2-yl)-1H-benzimidazole compounds as allosteric glucokinase activators.
Authors: Takahashi, K. / Hashimoto, N. / Nakama, C. / Kamata, K. / Sasaki, K. / Yoshimoto, R. / Ohyama, S. / Hosaka, H. / Maruki, H. / Nagata, Y. / Eiki, J. / Nishimura, T.
History
DepositionApr 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jul 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 1.4Mar 20, 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

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Assembly

Deposited unit
X: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2904
Polymers50,6111
Non-polymers6803
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.793, 79.793, 326.124
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: 50610.500 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 / 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-TK1 / 1-({5-[4-(methylsulfonyl)phenoxy]-2-pyridin-2-yl-1H-benzimidazol-6-yl}methyl)pyrrolidine-2,5-dione


Mass: 476.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H20N4O5S
#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.: 120 / 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: 2.96 Å3/Da / Density % sol: 58.46 % / Mosaicity: 0.441 °
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: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: May 25, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. obs: 34817 / % possible obs: 94.5 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.048 / Χ2: 1.161 / Net I/σ(I): 31.93
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.11-2.192.30.29229430.91683
2.19-2.272.90.22131950.88888.6
2.27-2.383.80.18333350.91892.9
2.38-2.550.14135150.9797.3
2.5-2.666.90.11435711.04498.7
2.66-2.8670.08635851.08898.4
2.86-3.1570.06235901.17598.2
3.15-3.616.80.04936231.36597.8
3.61-4.546.60.03936171.49695.9
4.54-506.20.02938431.17693.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.11→47.46 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.899 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.413 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1733 5 %RANDOM
Rwork0.232 ---
obs0.235 34816 94.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.33 Å2 / Biso mean: 39.888 Å2 / Biso min: 12.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.13 Å20 Å2
2--0.25 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.11→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3492 0 47 120 3659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0213596
X-RAY DIFFRACTIONr_angle_refined_deg2.0131.984839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3135445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.94224.035171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.05215658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3541530
X-RAY DIFFRACTIONr_chiral_restr0.1510.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022751
X-RAY DIFFRACTIONr_nbd_refined0.2280.21861
X-RAY DIFFRACTIONr_nbd_other0.4410.279
X-RAY DIFFRACTIONr_nbtor_refined0.310.22461
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3420.28
X-RAY DIFFRACTIONr_metal_ion_refined0.290.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4430.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.24
X-RAY DIFFRACTIONr_mcbond_it1.3221.52200
X-RAY DIFFRACTIONr_mcangle_it2.33823529
X-RAY DIFFRACTIONr_scbond_it3.48331430
X-RAY DIFFRACTIONr_scangle_it5.4534.51310
LS refinement shellResolution: 2.107→2.162 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 99 -
Rwork0.274 2011 -
all-2110 -
obs--79.41 %

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