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- PDB-4olh: Human GKRP Bound to AMG5106 and Sorbitol-6-Phosphate -

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Basic information

Entry
Database: PDB / ID: 4olh
TitleHuman GKRP Bound to AMG5106 and Sorbitol-6-Phosphate
ComponentsGlucokinase Regulatory Protein
KeywordsCARBOHYDRATE BINDING PROTEIN / SIS domain / Regulatory Protein / binds to and inhibits Glucokinase / Glucokinase / Liver
Function / homology
Function and homology information


glucose sensor activity / fructose-6-phosphate binding / carbohydrate derivative metabolic process / negative regulation of glucokinase activity / kinase inhibitor activity / urate metabolic process / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / response to fructose / regulation of glycolytic process ...glucose sensor activity / fructose-6-phosphate binding / carbohydrate derivative metabolic process / negative regulation of glucokinase activity / kinase inhibitor activity / urate metabolic process / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / response to fructose / regulation of glycolytic process / triglyceride homeostasis / response to glucose / protein localization to nucleus / intracellular glucose homeostasis / protein import into nucleus / 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-2TO / IODIDE ION / D-SORBITOL-6-PHOSPHATE / Glucokinase regulatory protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJordan, S.R. / Chmait, S.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Small molecule disruptors of the glucokinase-glucokinase regulatory protein interaction: 4. Exploration of a novel binding pocket.
Authors: Hong, F.T. / Norman, M.H. / Ashton, K.S. / Bartberger, M.D. / Chen, J. / Chmait, S. / Cupples, R. / Fotsch, C. / Jordan, S.R. / Lloyd, D.J. / Sivits, G. / Tadesse, S. / Hale, C. / St Jean, D.J.
History
DepositionJan 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)146,06937
Polymers140,6132
Non-polymers5,45635
Water1,874104
1
A: Glucokinase Regulatory Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,78116
Polymers70,3071
Non-polymers2,47415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glucokinase Regulatory Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,28821
Polymers70,3071
Non-polymers2,98220
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.344, 149.344, 133.138
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: 70306.617 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, 137 molecules

#2: Chemical ChemComp-2TO / 2-(2-{4-[(6-aminopyridin-3-yl)sulfonyl]piperazin-1-yl}-3,3'-bipyridin-5-yl)-1,1,1,3,3,3-hexafluoropropan-2-ol


Mass: 562.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H20F6N6O3S
#4: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Bis-tris, 0.2 M 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: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2012
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 65925 / Num. obs: 62523 / % possible obs: 94 % / Observed criterion σ(F): 1

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LY9

4ly9


Resolution: 2.4→39.4 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.522 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26556 3337 5.1 %RANDOM
Rwork0.21436 ---
obs0.21697 62523 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9075 0 156 104 9335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0199369
X-RAY DIFFRACTIONr_bond_other_d0.0020.029159
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.98212695
X-RAY DIFFRACTIONr_angle_other_deg0.883.00121016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88651169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72924.415376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.387151658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0031550
X-RAY DIFFRACTIONr_chiral_restr0.0930.21487
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110396
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022038
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_it4.4675.4254694
X-RAY DIFFRACTIONr_mcbond_other4.4665.4254693
X-RAY DIFFRACTIONr_mcangle_it6.5618.1245857
X-RAY DIFFRACTIONr_mcangle_other6.568.1245858
X-RAY DIFFRACTIONr_scbond_it4.5595.7974675
X-RAY DIFFRACTIONr_scbond_other4.4675.7934663
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7218.5336821
X-RAY DIFFRACTIONr_long_range_B_refined8.94642.77810624
X-RAY DIFFRACTIONr_long_range_B_other8.94642.7810625
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.399→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 250 -
Rwork0.364 4573 -
obs--99.03 %

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