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Yorodumi- PDB-4dch: Insights into Glucokinase Activation Mechanism: Observation of Mu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dch | ||||||
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Title | Insights into Glucokinase Activation Mechanism: Observation of Multiple Distinct Protein Conformations | ||||||
Components | Glucokinase | ||||||
Keywords | TRANSFERASE / GK Beta Cell / small molecule / open conformation / Kinase | ||||||
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 / NADP metabolic process / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / D-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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å | ||||||
Authors | Greasley, S.E. / Hickey, M. / Feng, J. / Garcia, E. | ||||||
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 | 4dch.cif.gz | 105.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dch.ent.gz | 79.3 KB | Display | PDB format |
PDBx/mmJSON format | 4dch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/4dch ftp://data.pdbj.org/pub/pdb/validation_reports/dc/4dch | HTTPS FTP |
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-Related 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: 53329.562 Da / Num. of mol.: 1 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-4DC / ( | ||
#4: Chemical | #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: 2.84 Å3/Da / Density % sol: 56.64 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 20% PEG 3350, 0.1A citrate pH 5.4, 0.2M ammonium iodide, 50mM glucose, VAPOR DIFFUSION, HANGING DROP, temperature 286K |
-Data collection
Diffraction | Mean temperature: 93 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2005 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. all: 54275 / Num. obs: 54275 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.068 / Χ2: 0.978 / Net I/σ(I): 11.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 0.516 / Cor.coef. Fo:Fc: 0.32
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2365 / WRfactor Rwork: 0.2058 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8509 / SU B: 2.417 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1169 / SU Rfree: 0.1149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.97 Å2 / Biso mean: 29.7263 Å2 / Biso min: 8.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.792→1.839 Å / Total num. of bins used: 20
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