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- PDB-3vf6: Glucokinase in complex with glucose and activator -

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Basic information

Entry
Database: PDB / ID: 3vf6
TitleGlucokinase in complex with glucose and activator
ComponentsGlucokinase
KeywordsTRANSFERASE/TRANSFERASE ACTIVATOR / catalysis reaction / TRANSFERASE / 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-0H6 / alpha-D-glucopyranose / Hexokinase-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.86 Å
AuthorsLiu, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Insights into Mechanism of Glucokinase Activation: OBSERVATION OF MULTIPLE DISTINCT PROTEIN CONFORMATIONS.
Authors: Liu, S. / Ammirati, M.J. / Song, X. / Knafels, J.D. / Zhang, J. / Greasley, S.E. / Pfefferkorn, J.A. / Qiu, X.
History
DepositionJan 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Other
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3May 9, 2012Group: Database references
Revision 1.4Jul 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Feb 28, 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
A: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5964
Polymers52,9961
Non-polymers6003
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.850, 82.230, 86.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 52996.188 Da / Num. of mol.: 1 / Fragment: UNP residues 12-465
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 / 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-0H6 / 6-({(2S)-3-cyclopentyl-2-[4-(trifluoromethyl)-1H-imidazol-1-yl]propanoyl}amino)pyridine-3-carboxylic acid


Mass: 396.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19F3N4O3
#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 / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 20mg/ml protein in 25 mM HEPES pH 7.0, 0.5 mM TCEP, 0.05 M NaCl, 40 mM glucose, 1 mM of activator, Crystallization drops in a 1:1 ratio were set up over wells containing 0.1 M Tris HCl, pH 7. ...Details: 20mg/ml protein in 25 mM HEPES pH 7.0, 0.5 mM TCEP, 0.05 M NaCl, 40 mM glucose, 1 mM of activator, Crystallization drops in a 1:1 ratio were set up over wells containing 0.1 M Tris HCl, pH 7.0, 80-200 mM glucose, and 19-26% PEG-4000, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→86 Å / Num. obs: 41536 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Biso Wilson estimate: 23.53 Å2

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Processing

SoftwareName: BUSTER / Version: 2.9.3 / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.86→52.81 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.9304 / SU R Cruickshank DPI: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 1924 4.98 %RANDOM
Rwork0.1758 ---
obs0.1773 38646 95.26 %-
Displacement parametersBiso mean: 29.99 Å2
Baniso -1Baniso -2Baniso -3
1--3.1922 Å20 Å20 Å2
2---1.1637 Å20 Å2
3---4.3559 Å2
Refine analyzeLuzzati coordinate error obs: 0.214 Å
Refinement stepCycle: LAST / Resolution: 1.86→52.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3535 0 41 246 3822
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013705HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.035010HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1377SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes103HARMONIC2
X-RAY DIFFRACTIONt_gen_planes567HARMONIC5
X-RAY DIFFRACTIONt_it3705HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion17.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion465SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4411SEMIHARMONIC4
LS refinement shellResolution: 1.86→1.91 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2496 73 4.61 %
Rwork0.2086 1512 -
all0.2106 1585 -
obs--95.26 %
Refinement TLS params.Method: refined / Origin x: -27.5676 Å / Origin y: -0.6975 Å / Origin z: 9.4241 Å
111213212223313233
T-0.0561 Å2-0.0179 Å20.0133 Å2--0.0895 Å2-0.0002 Å2---0.0797 Å2
L0.6729 °20.0261 °20.0198 °2-0.74 °2-0.0575 °2--0.9592 °2
S-0.0413 Å °-0.0009 Å °0.0574 Å °-0.0349 Å °0.0559 Å °0.006 Å °0.0318 Å °0.0201 Å °-0.0145 Å °

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