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- PDB-4dch: Insights into Glucokinase Activation Mechanism: Observation of Mu... -

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Basic information

Entry
Database: PDB / ID: 4dch
TitleInsights into Glucokinase Activation Mechanism: Observation of Multiple Distinct Protein Conformations
ComponentsGlucokinase
KeywordsTRANSFERASE / GK Beta Cell / small molecule / open conformation / Kinase
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 / calcium ion import / cellular response to leptin stimulus / 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-4DC / alpha-D-glucopyranose / IODIDE ION / Hexokinase-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å
AuthorsGreasley, S.E. / Hickey, M. / Feng, J. / Garcia, E.
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 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2May 9, 2012Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
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 1.5Feb 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)54,1425
Polymers53,3301
Non-polymers8124
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.917, 85.794, 72.939
Angle α, β, γ (deg.)90.000, 104.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glucokinase / / Hexokinase type IV / HK IV / Hexokinase-4 / HK4 / Hexokinase-D


Mass: 53329.562 Da / Num. of mol.: 1
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-4DC / (2R)-3-cyclopentyl-2-[4-(methylsulfonyl)phenyl]-N-(1,3-thiazol-2-yl)propanamide


Mass: 378.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N2O3S2
#4: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 20% PEG 3350, 0.1A citrate pH 5.4, 0.2M ammonium iodide, 50mM glucose, VAPOR DIFFUSION, HANGING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2005
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 54275 / Num. obs: 54275 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.068 / Χ2: 0.978 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.862.20.40841770.634175.5
1.86-1.942.70.32354040.668197.2
1.94-2.033.30.24955450.78199.7
2.03-2.133.70.17955580.8951100
2.13-2.273.70.13155951.0321100
2.27-2.443.70.10555511.1231100
2.44-2.693.70.08456101.1251100
2.69-3.083.70.06955911.1231100
3.08-3.883.60.05956141.036199.9
3.88-503.60.05256300.985199

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.516 / Cor.coef. Fo:Fc: 0.32
Highest resolutionLowest resolution
Rotation3 Å32.65 Å
Translation3 Å32.65 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Web-Icedata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2365 / WRfactor Rwork: 0.2058 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8509 / SU B: 2.417 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1169 / SU Rfree: 0.1149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 2747 5.1 %RANDOM
Rwork0.1981 ---
all0.1998 54252 --
obs0.1998 54252 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.97 Å2 / Biso mean: 29.7263 Å2 / Biso min: 8.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.69 Å2
2---0.2 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 39 311 3732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223485
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9774683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5435431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.43424165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24315645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2491530
X-RAY DIFFRACTIONr_chiral_restr0.1050.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022598
X-RAY DIFFRACTIONr_nbd_refined0.1980.21548
X-RAY DIFFRACTIONr_nbtor_refined0.2960.22367
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2262
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.211
X-RAY DIFFRACTIONr_mcbond_it1.0551.52171
X-RAY DIFFRACTIONr_mcangle_it1.69323440
X-RAY DIFFRACTIONr_scbond_it2.61431412
X-RAY DIFFRACTIONr_scangle_it4.1634.51243
LS refinement shellResolution: 1.792→1.839 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 138 -
Rwork0.27 2740 -
all-2878 -
obs--70.09 %

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