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- PDB-4no7: Human Glucokinase in complex with a nanomolar activator. -

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Basic information

Entry
Database: PDB / ID: 4no7
TitleHuman Glucokinase in complex with a nanomolar activator.
ComponentsGlucokinase
KeywordsTRANSFERASE/TRANSFERASE ACTIVATOR / Kinase / pancreas / TRANSFERASE-TRANSFERASE ACTIVATOR complex
Function / homology
Function and homology information


Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / detection of glucose / regulation of potassium ion transport / mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / canonical glycolysis / glucose 6-phosphate metabolic process / NADP metabolic process ...Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / detection of glucose / regulation of potassium ion transport / mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / canonical glycolysis / 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) / glucose binding / cellular response to leptin stimulus / calcium ion import / regulation of glycolytic process / Glycolysis / cellular glucose homeostasis / Regulation of gene expression in beta cells / regulation of insulin secretion / positive regulation of insulin secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / glycolytic process / cellular response to insulin stimulus / glucose homeostasis / mitochondrion / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Hexokinase-4, chordate / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase domain signature. / Hexokinase, N-terminal / Hexokinase / Hexokinase, binding site / Hexokinase, C-terminal / Hexokinase / Hexokinase domain profile. ...Hexokinase-4, chordate / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase domain signature. / Hexokinase, N-terminal / Hexokinase / Hexokinase, binding site / Hexokinase, C-terminal / Hexokinase / Hexokinase domain profile. / Hexokinase / 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-2N8 / alpha-D-glucopyranose / Hexokinase-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPetit, P. / Ferry, G. / Antoine, M. / Boutin, J.A. / Kotschy, A. / Perron-Sierra, F. / Mamelli, L. / Vuillard, L.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / 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
DepositionNov 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _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

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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)53,5983
Polymers52,9961
Non-polymers6022
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.300, 81.300, 85.500
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: Glucokinase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GCK / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P35557, glucokinase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / 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-2N8 / (2R)-2-[3-chloro-4-(methylsulfonyl)phenyl]-3-[(1R)-3-oxocyclopentyl]-N-(pyrazin-2-yl)propanamide


Mass: 421.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20ClN3O4S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 4000, 0.1M Hepes, 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: 1.0001 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2008
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 1.7→19.74 Å / Num. all: 50333 / Num. obs: 47815 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.77 / % possible all: 88.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V4S
Resolution: 1.7→19.74 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.476 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 3 / ESU R: 0.115 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 2517 5 %RANDOM
Rwork0.18959 ---
obs0.19125 47815 100 %-
all-50333 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.436 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3502 0 40 387 3929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223622
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.9794873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50923.966174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86215672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8411531
X-RAY DIFFRACTIONr_chiral_restr0.0960.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022718
X-RAY DIFFRACTIONr_nbd_refined0.2130.22141
X-RAY DIFFRACTIONr_nbtor_refined0.310.22560
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2409
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.219
X-RAY DIFFRACTIONr_mcbond_it0.8991.52265
X-RAY DIFFRACTIONr_mcangle_it1.44523552
X-RAY DIFFRACTIONr_scbond_it2.22831495
X-RAY DIFFRACTIONr_scangle_it3.6184.51317
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 179 -
Rwork0.251 3404 -
obs--100 %

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