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- PDB-4ly9: Human GKRP complexed to AMG-1694 [(2R)-1,1,1-trifluoro-2-{4-[(2S)... -

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Basic information

Entry
Database: PDB / ID: 4ly9
TitleHuman GKRP complexed to AMG-1694 [(2R)-1,1,1-trifluoro-2-{4-[(2S)-2-{[(3S)-3-methylmorpholin-4-yl]methyl}-4-(thiophen-2-ylsulfonyl)piperazin-1-yl]phenyl}propan-2-ol] and sorbitol-6-phosphate
ComponentsGlucokinase regulatory protein
KeywordsCarbohydrate Binding protein / Regulatory protein / disruptor ligand complex / SIS domains / GKRP binds to GK / Liver
Function / homology
Function and homology information


negative regulation of glucokinase activity / glucose sensor activity / fructose-6-phosphate binding / carbohydrate derivative metabolic process / kinase inhibitor activity / urate metabolic process / response to fructose / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / triglyceride homeostasis ...negative regulation of glucokinase activity / glucose sensor activity / fructose-6-phosphate binding / carbohydrate derivative metabolic process / kinase inhibitor activity / urate metabolic process / response to fructose / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / triglyceride homeostasis / enzyme inhibitor activity / response to glucose / protein import into nucleus / glucose homeostasis / carbohydrate binding / enzyme binding / mitochondrion / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
: / Glucokinase regulatory protein, second SIS domain / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / C-terminal lid domain of glucokinase regulatory protein / Glucokinase regulatory protein N-terminal SIS domain / Glucokinase regulatory protein family signature. / SIS domain / SIS domain profile. / SIS domain superfamily ...: / Glucokinase regulatory protein, second SIS domain / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / C-terminal lid domain of glucokinase regulatory protein / Glucokinase regulatory protein N-terminal SIS domain / Glucokinase regulatory protein family signature. / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1YY / IODIDE ION / D-SORBITOL-6-PHOSPHATE / Glucokinase regulatory protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsJordan, S.R.
CitationJournal: Nature / Year: 2013
Title: Antidiabetic effects of glucokinase regulatory protein small-molecule disruptors.
Authors: Lloyd, D.J. / St Jean, D.J. / Kurzeja, R.J. / Wahl, R.C. / Michelsen, K. / Cupples, R. / Chen, M. / Wu, J. / Sivits, G. / Helmering, J. / Komorowski, R. / Ashton, K.S. / Pennington, L.D. / ...Authors: Lloyd, D.J. / St Jean, D.J. / Kurzeja, R.J. / Wahl, R.C. / Michelsen, K. / Cupples, R. / Chen, M. / Wu, J. / Sivits, G. / Helmering, J. / Komorowski, R. / Ashton, K.S. / Pennington, L.D. / Fotsch, C. / Vazir, M. / Chen, K. / Chmait, S. / Zhang, J. / Liu, L. / Norman, M.H. / Andrews, K.L. / Bartberger, M.D. / Van, G. / Galbreath, E.J. / Vonderfecht, S.L. / Wang, M. / Jordan, S.R. / Veniant, M.M. / Hale, C.
History
DepositionJul 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucokinase regulatory protein
B: Glucokinase regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,76736
Polymers140,4992
Non-polymers5,26734
Water2,504139
1
A: Glucokinase regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,66016
Polymers70,2501
Non-polymers2,41115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glucokinase regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,10620
Polymers70,2501
Non-polymers2,85719
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.869, 148.869, 132.397
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Glucokinase regulatory protein / Glucokinase regulator


Mass: 70249.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GCKR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14397
#3: Sugar ChemComp-S6P / D-SORBITOL-6-PHOSPHATE / 1-O-PHOSPHONO-D-GLUCITOL / D-GLUCITOL-6-PHOSPHATE


Type: D-saccharide / Mass: 262.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H15O9P

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Non-polymers , 5 types, 171 molecules

#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-1YY / (2R)-1,1,1-trifluoro-2-{4-[(2S)-2-{[(3S)-3-methylmorpholin-4-yl]methyl}-4-(thiophen-2-ylsulfonyl)piperazin-1-yl]phenyl}propan-2-ol


Mass: 533.627 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H30F3N3O4S2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 3.01 Å3/Da / Density % sol: 59.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M bis-tris, 0.2M NaI, 16% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Apr 20, 2010 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→28.87 Å / Num. all: 65014 / Num. obs: 65340 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→28.87 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.907 / SU B: 7.471 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.299 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26999 3430 5 %RANDOM
Rwork0.21373 ---
obs0.21654 65014 98.8 %-
all-65340 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.277 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.35→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9075 0 150 139 9364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0199364
X-RAY DIFFRACTIONr_bond_other_d0.0010.029185
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.98112682
X-RAY DIFFRACTIONr_angle_other_deg0.93.00121048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23651169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72724.415376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.173151658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6571550
X-RAY DIFFRACTIONr_chiral_restr0.1020.21491
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110372
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022034
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0354.4374694
X-RAY DIFFRACTIONr_mcbond_other4.0324.4374693
X-RAY DIFFRACTIONr_mcangle_it5.9256.6395857
X-RAY DIFFRACTIONr_mcangle_other5.9256.6395858
X-RAY DIFFRACTIONr_scbond_it4.3774.8214670
X-RAY DIFFRACTIONr_scbond_other4.2554.8164662
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3867.0736814
X-RAY DIFFRACTIONr_long_range_B_refined8.36934.95410596
X-RAY DIFFRACTIONr_long_range_B_other8.37234.96510575
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 222 -
Rwork0.297 4496 -
obs--92.46 %

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