+Open data
-Basic information
Entry | Database: PDB / ID: 4l3q | ||||||
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Title | Crystal structure of glucokinase-activator complex | ||||||
Components | Glucokinase | ||||||
Keywords | Transferase/transferase activator / Glycolysis / Diabetes / Transferase-transferase activator complex | ||||||
Function / homology | Function and homology information Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / mannokinase activity / glucose sensor activity / regulation of potassium ion transport / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose catabolic process / glucose 6-phosphate metabolic process ...Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / mannokinase activity / glucose sensor activity / regulation of potassium ion transport / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose catabolic process / glucose 6-phosphate metabolic process / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / NADP metabolic process / glucose binding / cellular response to leptin stimulus / calcium ion import / canonical glycolysis / Glycolysis / regulation of glycolytic process / intracellular glucose homeostasis / Regulation of gene expression in beta cells / regulation of insulin secretion / positive regulation of glycogen biosynthetic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / response to glucose / glycolytic process / positive regulation of insulin secretion / cellular response to insulin stimulus / glucose metabolic process / glucose homeostasis / mitochondrion / nucleoplasm / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.7 Å | ||||||
Authors | Gajiwala, K.S. / Filipski, K.J. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2013 Title: Pyrimidone-based series of glucokinase activators with alternative donor-acceptor motif. Authors: Filipski, K.J. / Guzman-Perez, A. / Bian, J. / Perreault, C. / Aspnes, G.E. / Didiuk, M.T. / Dow, R.L. / Hank, R.F. / Jones, C.S. / Maguire, R.J. / Tu, M. / Zeng, D. / Liu, S. / Knafels, J.D. ...Authors: Filipski, K.J. / Guzman-Perez, A. / Bian, J. / Perreault, C. / Aspnes, G.E. / Didiuk, M.T. / Dow, R.L. / Hank, R.F. / Jones, C.S. / Maguire, R.J. / Tu, M. / Zeng, D. / Liu, S. / Knafels, J.D. / Litchfield, J. / Atkinson, K. / Derksen, D.R. / Bourbonais, F. / Gajiwala, K.S. / Hickey, M. / Johnson, T.O. / Humphries, P.S. / Pfefferkorn, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l3q.cif.gz | 101.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l3q.ent.gz | 76.9 KB | Display | PDB format |
PDBx/mmJSON format | 4l3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/4l3q ftp://data.pdbj.org/pub/pdb/validation_reports/l3/4l3q | HTTPS FTP |
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-Related structure data
Related structure data | 1v4sS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 51163.164 Da / Num. of mol.: 1 / Fragment: UNP residues 16-465 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GCK / Production host: Escherichia coli (E. coli) / References: UniProt: P35557, glucokinase |
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#2: Sugar | ChemComp-GLC / |
#3: Chemical | ChemComp-926 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K / PH range: 7.0-8.0 |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 2004 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 17490 / Num. obs: 17045 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.042 / Net I/σ(I): 32.3 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 9.3 / Num. unique all: 1678 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1V4S Resolution: 2.7→39.84 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.866 / SU B: 14.604 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R: 1.089 / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.461 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→39.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20 /
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