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- PDB-4mro: Human GKRP bound to AMG-5980 and S6P -

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Basic information

Entry
Database: PDB / ID: 4mro
TitleHuman GKRP bound to AMG-5980 and S6P
ComponentsGlucokinase regulatory protein
KeywordsTransferase Inhibitor / SIS domains / Regulatory protein / Glucokinase / phospho-fructose
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
IODIDE ION / Chem-MG0 / D-SORBITOL-6-PHOSPHATE / Glucokinase regulatory protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSt Jean, D.J. / Ashton, K.S. / Bartberger, M.D. / Chen, J. / Chmait, S. / Cupples, R. / Galbreath, E. / Helmering, J. / Jordan, S.R. / Liu, L. ...St Jean, D.J. / Ashton, K.S. / Bartberger, M.D. / Chen, J. / Chmait, S. / Cupples, R. / Galbreath, E. / Helmering, J. / Jordan, S.R. / Liu, L. / Kunz, K. / Michelsen, K. / Nishimura, N. / Pennington, L.D. / Poon, S.F. / Sivits, G. / Stec, M.M. / Tamayo, N. / Van, G. / Yang, K. / Norman, M.H. / Fotsch, C. / LLoyd, D.J. / Hale, C.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Small molecule disruptors of the glucokinase-glucokinase regulatory protein interaction: 2. Leveraging structure-based drug design to identify analogues with improved pharmacokinetic profiles.
Authors: St Jean, D.J. / Ashton, K.S. / Bartberger, M.D. / Chen, J. / Chmait, S. / Cupples, R. / Galbreath, E. / Helmering, J. / Hong, F.T. / Jordan, S.R. / Liu, L. / Kunz, R.K. / Michelsen, K. / ...Authors: St Jean, D.J. / Ashton, K.S. / Bartberger, M.D. / Chen, J. / Chmait, S. / Cupples, R. / Galbreath, E. / Helmering, J. / Hong, F.T. / Jordan, S.R. / Liu, L. / Kunz, R.K. / Michelsen, K. / Nishimura, N. / Pennington, L.D. / Poon, S.F. / Reid, D. / Sivits, G. / Stec, M.M. / Tadesse, S. / Tamayo, N. / Van, G. / Yang, K.C. / Zhang, J. / Norman, M.H. / Fotsch, C. / Lloyd, D.J. / Hale, C.
History
DepositionSep 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)145,40335
Polymers140,3572
Non-polymers5,04633
Water1,24369
1
A: Glucokinase regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,41315
Polymers70,1781
Non-polymers2,23514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glucokinase regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,99020
Polymers70,1781
Non-polymers2,81119
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.129, 149.129, 132.383
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: 70178.492 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, 100 molecules

#2: Chemical ChemComp-MG0 / 2-(4-{4-[(6-aminopyridin-3-yl)sulfonyl]piperazin-1-yl}phenyl)-1,1,1,3,3,3-hexafluoropropan-2-ol / AMG-5980


Mass: 484.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18F6N4O3S
#4: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 25 / 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.: 69 / 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: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: Well buffer: 0.1M Bis-tris, 0.2M NaI, 16% PEG 8K, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT
DetectorType: RIGAKU SATURN 92 / Detector: CCD
RadiationMonochromator: confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→26 Å / Num. all: 77422 / Num. obs: 72687 / % possible obs: 93.9 % / 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
Starting model: Internal structure

Resolution: 2.2→26 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.771 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.272 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28816 3826 5 %RANDOM
Rwork0.22977 ---
obs0.23263 72687 90.34 %-
all-77422 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.834 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9075 0 142 69 9286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0199355
X-RAY DIFFRACTIONr_bond_other_d0.0010.029155
X-RAY DIFFRACTIONr_angle_refined_deg1.8791.9812675
X-RAY DIFFRACTIONr_angle_other_deg0.9113.00121012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.24851169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17224.415376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.436151658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1581550
X-RAY DIFFRACTIONr_chiral_restr0.1010.21487
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110380
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_it4.2874.9214694
X-RAY DIFFRACTIONr_mcbond_other4.2854.9214693
X-RAY DIFFRACTIONr_mcangle_it6.0477.3685857
X-RAY DIFFRACTIONr_mcangle_other6.0477.3685858
X-RAY DIFFRACTIONr_scbond_it4.4915.2574661
X-RAY DIFFRACTIONr_scbond_other4.3975.2494649
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3527.7436801
X-RAY DIFFRACTIONr_long_range_B_refined8.1639.15210688
X-RAY DIFFRACTIONr_long_range_B_other8.1639.15310689
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 133 -
Rwork0.351 2452 -
obs--41.65 %

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