+Open data
-Basic information
Entry | Database: PDB / ID: 1v4t | ||||||
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Title | Crystal structure of human glucokinase | ||||||
Components | glucokinase isoform 2 | ||||||
Keywords | TRANSFERASE / hexokinase IV / allosteric enzyme / diabetes | ||||||
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 / calcium ion import / cellular response to leptin stimulus / 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: 3.4 Å | ||||||
Authors | Kamata, K. / Mitsuya, M. / Nishimura, T. / Eiki, J. / Nagata, Y. | ||||||
Citation | 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 | 1v4t.cif.gz | 96.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v4t.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 1v4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/1v4t ftp://data.pdbj.org/pub/pdb/validation_reports/v4/1v4t | HTTPS FTP |
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-Related structure data
Related structure data | 1v4sSC S: Starting model for refinement C: citing same article (ref.) |
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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: 50610.500 Da / Num. of mol.: 1 / Fragment: RESIDUES 15-465 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): DH5A / References: UniProt: P35557, hexokinase | ||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: 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: 4.61 Å3/Da / Density % sol: 73.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: Ammonium sulfate, Bicine, Sodium chloride, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 9, 2002 |
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: 3.4→87.71 Å / Num. obs: 12925 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 77.8 Å2 / Rsym value: 0.088 / Net I/σ(I): 6.84 |
Reflection shell | Resolution: 3.4→3.58 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.214 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1V4S Resolution: 3.4→48.43 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2102820.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 14.7978 Å2 / ksol: 0.337635 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.4→48.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.61 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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