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Yorodumi- PDB-4dhy: Crystal structure of human glucokinase in complex with glucose an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dhy | ||||||
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Title | Crystal structure of human glucokinase in complex with glucose and activator | ||||||
Components | Glucokinase | ||||||
Keywords | TRANSFERASE/TRANSFERASE ACTIVATOR / DIABETES MELLITUS / DISEASE MUTATION / GLYCOLYSIS / TRANSFERASE / 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: 2.38 Å | ||||||
Authors | Liu, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Insights into Mechanism of Glucokinase Activation: OBSERVATION OF MULTIPLE DISTINCT PROTEIN CONFORMATIONS. Authors: Liu, S. / Ammirati, M.J. / Song, X. / Knafels, J.D. / Zhang, J. / Greasley, S.E. / Pfefferkorn, J.A. / Qiu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dhy.cif.gz | 193.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dhy.ent.gz | 151.3 KB | Display | PDB format |
PDBx/mmJSON format | 4dhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/4dhy ftp://data.pdbj.org/pub/pdb/validation_reports/dh/4dhy | HTTPS FTP |
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-Related structure data
Related structure data | 3vevC 3veyC 3vf6C 4dchC 3f9mS C: citing same article (ref.) 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: 52939.133 Da / Num. of mol.: 1 / Fragment: UNP residues 12-465 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-S41 / |
#4: Chemical | ChemComp-NA / |
#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: 2.24 Å3/Da / Density % sol: 45.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 5, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→52.9 Å / Num. obs: 18951 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 35.87 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.38→2.51 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2562 / % possible all: 92.5 |
-Processing
Software | Name: BUSTER / Version: 2.11.2 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3F9M Resolution: 2.38→52.9 Å / Cor.coef. Fo:Fc: 0.9292 / Cor.coef. Fo:Fc free: 0.8868 / SU R Cruickshank DPI: 0.435 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 29.19 Å2
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Refine analyze | Luzzati coordinate error obs: 0.288 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→52.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.51 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: -27.5812 Å / Origin y: -0.8077 Å / Origin z: 9.5699 Å
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