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- PDB-3idh: Human pancreatic glucokinase in complex with glucose -

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Basic information

Entry
Database: PDB / ID: 3idh
TitleHuman pancreatic glucokinase in complex with glucose
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) / 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
alpha-D-glucopyranose / : / Hexokinase-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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 21, 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: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_residues / 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
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)53,2153
Polymers52,9961
Non-polymers2192
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.510, 81.970, 86.950
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) / 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 / 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-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.2 Å3/Da / Density % sol: 44.16 %
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: 2.14→25 Å / Num. obs: 26185 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.08 / Rsym value: 0.09 / Net I/σ(I): 16.9
Reflection shellResolution: 2.14→2.26 Å / Redundancy: 3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3 / Num. unique all: 3739 / Rsym value: 0.48 / % possible all: 98.6

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Processing

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

1v4s


Resolution: 2.14→15 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.652 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; 2. RESIDUES 140-142 BELONG TO AN UNFOLDED GROUP, AND THE OCCUPANCIES WERE SET TO 0.
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 1321 5.1 %RANDOM
Rwork0.18886 ---
obs0.19041 24739 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.912 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20 Å2
2---0.7 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.14→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3557 0 13 225 3795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223645
X-RAY DIFFRACTIONr_bond_other_d00.022530
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9684902
X-RAY DIFFRACTIONr_angle_other_deg4.25836140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.845458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15524.078179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.16115677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5811531
X-RAY DIFFRACTIONr_chiral_restr0.0830.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024084
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02748
X-RAY DIFFRACTIONr_nbd_refined0.2070.2790
X-RAY DIFFRACTIONr_nbd_other0.2510.22442
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21737
X-RAY DIFFRACTIONr_nbtor_other0.1090.21790
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2208
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2020.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3630.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6191.52241
X-RAY DIFFRACTIONr_mcbond_other01.5939
X-RAY DIFFRACTIONr_mcangle_it1.10723596
X-RAY DIFFRACTIONr_scbond_it1.64631404
X-RAY DIFFRACTIONr_scangle_it2.4884.51303
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.14→2.194 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 100 -
Rwork0.207 1741 -
obs--97.05 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8902-0.24251.98321.084-0.34962.6503-0.0769-0.21180.18760.11780.03770.0715-0.0435-0.16920.0392-0.10180.00480.0397-0.0482-0.0057-0.0604-36.2174.40216.681
24.03341.47611.59046.88312.96857.06310.05030.01820.6154-0.2230.2368-0.3724-0.3770.2466-0.2871-0.05480.02880.1106-0.1116-0.0040.0172-9.46-4.5734.643
31.0103-1.0593-0.37614.48330.7911.6758-0.0023-0.01380.0072-0.0460.0468-0.35480.15430.1666-0.0444-0.01040.02580.0139-0.05420.0075-0.0495-13.612-16.2829.815
40.529-0.26560.17041.23280.090.9331-0.0207-0.0060.01810.09160.0819-0.1489-0.03850.1-0.0613-0.0360.0078-0.0077-0.0284-0.0204-0.0266-21.2231.17220.383
51.9365-0.54081.14540.2948-0.50512.22140.0286-0.0005-0.053-0.08220.09070.11150.0971-0.1674-0.1193-0.0292-0.0308-0.037-0.0220.01560.0015-43.681-3.3012.849
62.7620.72991.58266.53721.22552.4217-0.24080.414-0.0667-0.54210.2275-0.3848-0.06940.29710.01330.0016-0.07780.0051-0.01240.0344-0.1219-38.1342.307-10.156
72.63230.8233.71340.65071.0415.9858-0.2461-0.11490.2571-0.03530.08590.1142-0.3452-0.12220.1602-0.01260.0101-0.0222-0.05690.0070.0023-35.8829.6948.753
82.3568-0.45760.18142.99931.70142.605-0.00830.06120.202-0.14270.0718-0.0191-0.31060.0212-0.0635-0.0094-0.03520.0371-0.10470.0081-0.0195-26.94813.98812.31
94.3152-6.21730.867112.8496-2.32713.00210.02210.25060.4895-0.6643-0.1325-1.28860.14030.40690.1104-0.1278-0.05270.0808-0.0426-0.01550.0795-11.3673.12711.26
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 70
2X-RAY DIFFRACTION2A71 - 115
3X-RAY DIFFRACTION3A116 - 196
4X-RAY DIFFRACTION4A197 - 270
5X-RAY DIFFRACTION5A271 - 320
6X-RAY DIFFRACTION6A321 - 357
7X-RAY DIFFRACTION7A358 - 399
8X-RAY DIFFRACTION8A400 - 436
9X-RAY DIFFRACTION9A437 - 457

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