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- PDB-4px3: Human GKRP bound to AMG-3295 and Sorbitol-6-phosphate -

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Basic information

Entry
Database: PDB / ID: 4px3
TitleHuman GKRP bound to AMG-3295 and Sorbitol-6-phosphate
ComponentsGlucokinase regulatory protein
Keywordssugar binding protein/inhibitor / SIS domain containing protein / Regulatory protein - binds to and inhibits glucokinase / sugar binding protein-inhibitor complex
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-2WX / IODIDE ION / D-SORBITOL-6-PHOSPHATE / Glucokinase regulatory protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsJordan, S.R. / Chmait, S.
CitationJournal: To be Published
Title: Discovery and Structure-Guided Optimization of Diarylmethanesulfonamide Disruptors of GK-GKRP Binding
Authors: Pennington, L.D. / Bartberger, M.D. / Croghan, M.D. / Andrews, K.L. / Ashton, K.S. / Bourbeau, M.P. / Chen, J. / Chmait, S. / Cupples, R. / Fotsch, C.
History
DepositionMar 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 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)146,10839
Polymers140,6132
Non-polymers5,49537
Water1,71195
1
A: Glucokinase regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,70516
Polymers70,3071
Non-polymers2,39815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glucokinase regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,40423
Polymers70,3071
Non-polymers3,09722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.873, 148.873, 132.326
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 / GKRP / 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, 130 molecules

#2: Chemical ChemComp-2WX / N-[(R)-1-benzothiophen-2-yl(2-chlorophenyl)methyl]-3,4-dihydro-2H-1,5-benzodioxepine-7-sulfonamide


Mass: 486.003 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H20ClNO4S2
#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.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 59.14 %
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: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.43→29.9 Å / Num. all: 62314 / Num. obs: 59121 / % possible obs: 94.8 % / 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: 2.43→24.94 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.662 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.317 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25759 3151 5.1 %RANDOM
Rwork0.19581 ---
obs0.19894 59121 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.163 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.43→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9075 0 154 95 9324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0199367
X-RAY DIFFRACTIONr_bond_other_d0.0010.029161
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.98112683
X-RAY DIFFRACTIONr_angle_other_deg0.8673.00121018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63251169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13824.415376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.442151658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0891550
X-RAY DIFFRACTIONr_chiral_restr0.0910.21483
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110390
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_it4.5945.3584694
X-RAY DIFFRACTIONr_mcbond_other4.5945.3574693
X-RAY DIFFRACTIONr_mcangle_it6.7588.0215857
X-RAY DIFFRACTIONr_mcangle_other6.7588.0225858
X-RAY DIFFRACTIONr_scbond_it4.8675.8784673
X-RAY DIFFRACTIONr_scbond_other4.8185.874653
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2758.6096797
X-RAY DIFFRACTIONr_long_range_B_refined9.74242.76710684
X-RAY DIFFRACTIONr_long_range_B_other9.74242.76810685
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.433→2.496 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 242 -
Rwork0.264 4294 -
obs--100 %

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