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Yorodumi- PDB-4lc9: Structural Basis for Regulation of Human Glucokinase by Glucokina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lc9 | ||||||
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Title | Structural Basis for Regulation of Human Glucokinase by Glucokinase Regulatory Protein | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE REGULATOR / Type 2 Diabetes / TRANSFERASE-TRANSFERASE REGULATOR complex | ||||||
Function / homology | Function and homology information negative regulation of hexokinase activity / detection of glucose / positive regulation of glucokinase activity / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / negative regulation of glucokinase activity / fructose-6-phosphate binding / mannokinase activity / glucose sensor activity / regulation of potassium ion transport ...negative regulation of hexokinase activity / detection of glucose / positive regulation of glucokinase activity / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / negative regulation of glucokinase activity / fructose-6-phosphate binding / mannokinase activity / glucose sensor activity / regulation of potassium ion transport / urate metabolic process / hexokinase / fructokinase activity / carbohydrate derivative metabolic process / carbohydrate phosphorylation / glucokinase activity / glucose catabolic process / glucose 6-phosphate metabolic process / response to fructose / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / NADP metabolic process / triglyceride homeostasis / glucose binding / cellular response to leptin stimulus / calcium ion import / canonical glycolysis / enzyme inhibitor activity / Glycolysis / regulation of glycolytic process / intracellular glucose homeostasis / Regulation of gene expression in beta cells / regulation of insulin secretion / protein localization to nucleus / 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 / protein import into nucleus / cellular response to insulin stimulus / glucose metabolic process / glucose homeostasis / carbohydrate binding / protein domain specific binding / enzyme binding / mitochondrion / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Beck, T. / Miller, B.G. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Structural basis for regulation of human glucokinase by glucokinase regulatory protein. Authors: Beck, T. / Miller, B.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lc9.cif.gz | 204.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lc9.ent.gz | 161 KB | Display | PDB format |
PDBx/mmJSON format | 4lc9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/4lc9 ftp://data.pdbj.org/pub/pdb/validation_reports/lc/4lc9 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 70152.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gckr / Production host: Escherichia coli (E. coli) / References: UniProt: Q07071 |
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#2: Protein | Mass: 53204.465 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 |
#3: Sugar | ChemComp-F6P / |
#4: Chemical | ChemComp-NA / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: Crystals were obtained at 20 C by mixing 200 nL of GCK-GKRP-F6P complex solution with 100 nL of reservoir solution containing 0.1 M HEPES, pH 7.1, and 8% w/v PEG 6000, VAPOR DIFFUSION, ...Details: Crystals were obtained at 20 C by mixing 200 nL of GCK-GKRP-F6P complex solution with 100 nL of reservoir solution containing 0.1 M HEPES, pH 7.1, and 8% w/v PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2012 |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→48.93 Å / Num. all: 18995 / Num. obs: 18946 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.73 / Redundancy: 6.5 % / Rmerge(I) obs: 0.0712 / Net I/σ(I): 12.93 |
Reflection shell | Resolution: 3.4→3.5 Å / Redundancy: 6.23 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 1.73 / % possible all: 99.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→48.929 Å / SU ML: 0.57 / σ(F): 1.33 / Phase error: 34.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→48.929 Å
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Refine LS restraints |
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LS refinement shell |
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