+Open data
-Basic information
Entry | Database: PDB / ID: 3fr0 | ||||||
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Title | Human glucokinase in complex with 2-amino benzamide activator | ||||||
Components | Glucokinase | ||||||
Keywords | TRANSFERASE / Hexokinase IV / Allosteric enzyme / Diabetes / Alternative splicing / ATP-binding / Diabetes mellitus / Disease mutation / Glycolysis / Kinase / Nucleotide-binding / Polymorphism | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Kamata, K. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: Identification of novel and potent 2-amino benzamide derivatives as allosteric glucokinase activators Authors: Nishimura, T. / Iino, T. / Mitsuya, M. / Bamba, M. / Watanabe, H. / Tsukahara, D. / Kamata, K. / Sasaki, K. / Ohyama, S. / Hosaka, H. / Futamura, M. / Nagata, Y. / Eiki, J. #1: Journal: Structure / Year: 2004 Title: Structural basis for allosteric regulation of the monomeric allosteric enzyme human glucokinase Authors: Kamata, K. / Mitsuya, M. / Nishimura, T. / Eiki, J. / Nagata, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fr0.cif.gz | 106.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fr0.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 3fr0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/3fr0 ftp://data.pdbj.org/pub/pdb/validation_reports/fr/3fr0 | HTTPS FTP |
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-Related structure data
Related structure data | 1v4sS 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: 50978.902 Da / Num. of mol.: 1 / Fragment: Enzyme, UNP residues 12-466 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFLAG-CTC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alfa / References: UniProt: P35557, glucokinase |
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#2: Sugar | ChemComp-GLC / |
#3: Chemical | ChemComp-AJB / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE FOR THIS PROTEIN IS BASED ON ISOFORM 2 OF HXK4_HUMAN (UNIPROTKB/SWISS-PROT P35557). |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 30 % PEG 1500, HEPES, PH 6.6, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Oct 2, 2001 / Details: mirrors |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 17948 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Redundancy: 20.1 % / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 59.8 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 21.2 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 18.4 / Num. unique all: 2105 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1V4S Resolution: 2.7→40.07 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 2281970 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.639 Å2 / ksol: 0.343 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.69 Å2 / Biso mean: 44.146 Å2 / Biso min: 12.57 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→40.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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