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- PDB-4px2: Human GKRP bound to AMG2882 and Sorbitol-6-Phosphate -

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Basic information

Entry
Database: PDB / ID: 4px2
TitleHuman GKRP bound to AMG2882 and Sorbitol-6-Phosphate
ComponentsGlucokinase regulatory protein
Keywordssugar binding protein/inhibitor / SIS domain containing protein / Regulatory protein - Binds to and inhibits Glucokinase / Glucokinase / sugar binding protein-inhibitor complex
Function / homology
Function and homology information


negative regulation of glucokinase activity / fructose-6-phosphate binding / glucose sensor activity / urate metabolic process / kinase inhibitor activity / carbohydrate derivative 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 / fructose-6-phosphate binding / glucose sensor activity / urate metabolic process / kinase inhibitor activity / carbohydrate derivative 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 / carbohydrate metabolic process / enzyme binding / mitochondrion / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
C-terminal lid domain of glucokinase regulatory protein / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / 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-2WY / IODIDE ION / D-SORBITOL-6-PHOSPHATE / Glucokinase regulatory protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)146,22241
Polymers140,6132
Non-polymers5,60939
Water2,720151
1
A: Glucokinase regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,74617
Polymers70,3071
Non-polymers2,43916
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glucokinase regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,47624
Polymers70,3071
Non-polymers3,17023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.155, 148.155, 131.434
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, 188 molecules

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


Mass: 435.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H21NO5S
#4: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Bis-tris,0.2M NaI,16% PEG8000, 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 SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Apr 4, 2010 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→27 Å / Num. all: 88141 / Num. obs: 82965 / % possible obs: 94.1 % / 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: 2.15→27 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.333 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2786 4370 5 %RANDOM
Rwork0.22735 ---
obs0.22994 82965 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.555 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.15→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9075 0 160 151 9386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0199371
X-RAY DIFFRACTIONr_bond_other_d0.0020.029175
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.98112683
X-RAY DIFFRACTIONr_angle_other_deg0.8893.00121048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9351169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20824.415376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.72151658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1881550
X-RAY DIFFRACTIONr_chiral_restr0.0990.21484
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110388
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_it4.2834.7554694
X-RAY DIFFRACTIONr_mcbond_other4.2844.7554693
X-RAY DIFFRACTIONr_mcangle_it6.087.1135857
X-RAY DIFFRACTIONr_mcangle_other6.087.1135858
X-RAY DIFFRACTIONr_scbond_it4.4985.1614677
X-RAY DIFFRACTIONr_scbond_other4.4315.1554661
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4777.5916803
X-RAY DIFFRACTIONr_long_range_B_refined8.48838.02610831
X-RAY DIFFRACTIONr_long_range_B_other8.48938.02610831
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 310 -
Rwork0.361 5669 -
obs--91.59 %

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