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- PDB-3id8: Ternary complex of human pancreatic glucokinase crystallized with... -

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Basic information

Entry
Database: PDB / ID: 3id8
TitleTernary complex of human pancreatic glucokinase crystallized with activator, glucose and AMP-PNP
ComponentsGlucokinase
KeywordsTRANSFERASE / Glucokinase / Hexokinase IV / ATP-binding / Diabetes mellitus / Disease mutation / Glycolysis / Kinase / Nucleotide-binding
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 / 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 / mannokinase activity / regulation of potassium ion transport / 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 / calcium ion import / canonical glycolysis / 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 / glucose metabolic process / cellular response to insulin stimulus / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / alpha-D-glucopyranose / : / Chem-MRK / Hexokinase-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPetit, P. / Gluais, L. / Lagarde, A. / Boutin, J.A. / Ferry, G. / Vuillard, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: The active conformation of human glucokinase is not altered by allosteric activators
Authors: Petit, P. / Antoine, M. / Ferry, G. / Boutin, J.A. / Lagarde, A. / Gluais, L. / Vincentelli, R. / Vuillard, L.
History
DepositionJul 20, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 9, 2011Group: Database references
Revision 1.3Apr 25, 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 / 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 1.5Nov 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)54,0956
Polymers52,9961
Non-polymers1,0995
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.000, 82.600, 86.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / 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

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Non-polymers , 5 types, 129 molecules

#3: Chemical ChemComp-MRK / 2-AMINO-4-FLUORO-5-[(1-METHYL-1H-IMIDAZOL-2-YL)SULFANYL]-N-(1,3-THIAZOL-2-YL)BENZAMIDE


Mass: 349.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12FN5OS2
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→19.94 Å / Num. all: 19433 / Num. obs: 18612 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.09 / Rsym value: 0.08 / Net I/σ(I): 16.8
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 5.2 / Num. unique all: 2015 / Rsym value: 0.39 / % possible all: 91.5

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V4S

1v4s


Resolution: 2.4→19.94 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.899 / Cross valid method: THROUGHOUT / ESU R: 0.521 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27908 966 5 %RANDOM
Rwork0.20123 ---
obs0.20512 18338 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.177 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2--1.03 Å20 Å2
3----1.94 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3535 0 68 125 3728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223684
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9864962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8645454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08723.898177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.65115675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3411532
X-RAY DIFFRACTIONr_chiral_restr0.0940.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022761
X-RAY DIFFRACTIONr_nbd_refined0.230.21690
X-RAY DIFFRACTIONr_nbtor_refined0.30.22443
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2172
X-RAY DIFFRACTIONr_metal_ion_refined0.2030.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3990.28
X-RAY DIFFRACTIONr_mcbond_it0.6121.52227
X-RAY DIFFRACTIONr_mcangle_it1.15823575
X-RAY DIFFRACTIONr_scbond_it1.62531457
X-RAY DIFFRACTIONr_scangle_it2.6984.51384
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 70 -
Rwork0.227 1321 -
obs--100 %

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