+Open data
-Basic information
Entry | Database: PDB / ID: 4no7 | ||||||
---|---|---|---|---|---|---|---|
Title | Human Glucokinase in complex with a nanomolar activator. | ||||||
Components | Glucokinase | ||||||
Keywords | TRANSFERASE/TRANSFERASE ACTIVATOR / Kinase / pancreas / TRANSFERASE-TRANSFERASE ACTIVATOR complex | ||||||
Function / homology | Function and homology information Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / glucose sensor activity / regulation of potassium ion transport / mannokinase activity / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucose catabolic process / glucokinase activity / glucose 6-phosphate metabolic process ...Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / glucose sensor activity / regulation of potassium ion transport / mannokinase activity / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucose catabolic process / glucokinase activity / 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 / 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 / Resolution: 1.7 Å | ||||||
Authors | Petit, P. / Ferry, G. / Antoine, M. / Boutin, J.A. / Kotschy, A. / Perron-Sierra, F. / Mamelli, L. / Vuillard, L. | ||||||
Citation | Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2011 Title: The active conformation of human glucokinase is not altered by allosteric activators. Authors: Petit, P. / Antoine, M. / Ferry, G. / Boutin, J.A. / Lagarde, A. / Gluais, L. / Vincentelli, R. / Vuillard, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4no7.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4no7.ent.gz | 83.3 KB | Display | PDB format |
PDBx/mmJSON format | 4no7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4no7_validation.pdf.gz | 788 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4no7_full_validation.pdf.gz | 797.6 KB | Display | |
Data in XML | 4no7_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 4no7_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/4no7 ftp://data.pdbj.org/pub/pdb/validation_reports/no/4no7 | HTTPS FTP |
-Related structure data
Related structure data | 3f9mC 3fguC 3id8C 3idhC 1v4sS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 52996.188 Da / Num. of mol.: 1 / Fragment: Glucokinase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GCK / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P35557, glucokinase |
---|---|
#2: Sugar | ChemComp-GLC / |
#3: Chemical | ChemComp-2N8 / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.42 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% PEG 4000, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0001 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2008 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0001 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.74 Å / Num. all: 50333 / Num. obs: 47815 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.77 / % possible all: 88.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1V4S Resolution: 1.7→19.74 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.476 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 3 / ESU R: 0.115 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 24.436 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→19.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
|