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Yorodumi- PDB-4ixc: Crystal structure of Human Glucokinase in complex with a small mo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ixc | ||||||
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Title | Crystal structure of Human Glucokinase in complex with a small molecule activator. | ||||||
Components | Glucokinase isoform 3 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Allosteric Regulation / Binding Sites / Catalytic Domain / Diabetes Mellitus / Type 2 / Enzyme Activators / Glucokinase / Hexokinase / Humans / Models / Molecular / Mutation / Protein Conformation / TRANSFERASE-TRANSFERASE INHIBITOR 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ogg, D.J. / Hargreaves, D. / Gerhardt, S. | ||||||
Citation | Journal: To be Published Title: Matched triplicate design sets in the optimisation of glucokinase activators maximising medicinal chemistry information content Authors: Waring, M.J. / Bennett, S.N.L. / Boyd, S. / Campbell, L. / Davies, R.D.M. / Gerhardt, S. / Hargreaves, D. / G Martin, N. / Robb, G.R. / Wilkinson, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ixc.cif.gz | 186.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ixc.ent.gz | 150.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ixc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/4ixc ftp://data.pdbj.org/pub/pdb/validation_reports/ix/4ixc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 50807.680 Da / Num. of mol.: 1 / Fragment: GLUCOKINASE / Mutation: E27A E28A E51A E52A 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: Chemical | ChemComp-NA / |
#3: Sugar | ChemComp-GLC / |
#4: Chemical | ChemComp-1JD / ( |
#5: 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: 2.54 Å3/Da / Density % sol: 51.67 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 20% glucose, 10-18% Peg8000, 200mM sodium acetate, MMT 100mM pH7.0-8.5, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 13, 2008 / Details: mirrors |
Radiation | Monochromator: Osmic confocal multilayer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→54.8 Å / Num. all: 34425 / Num. obs: 31632 / % possible obs: 91.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.82 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.84 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 1.7 / Num. unique all: 3406 / % possible all: 51.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25.89 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.995 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.185 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.426 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 63.1923 Å / Origin y: 25.7267 Å / Origin z: 0.2043 Å
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