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- PDB-6ul7: Structure of human ketohexokinase-C in complex with fructose, NO3... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ul7 | ||||||
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Title | Structure of human ketohexokinase-C in complex with fructose, NO3, and osthole | ||||||
![]() | Ketohexokinase | ||||||
![]() | TRANSFERASE / beta-clasp / sugar kinase / PfKB family / KHK / ketohexokinase / fructose / osthole | ||||||
Function / homology | ![]() Essential fructosuria / ketohexokinase / Fructose catabolism / ketohexokinase activity / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose ...Essential fructosuria / ketohexokinase / Fructose catabolism / ketohexokinase activity / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose / response to insulin / extracellular exosome / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gasper, W.C. / Gardner, S. / Allen, K.N. / Tolan, D.R. | ||||||
![]() | ![]() Title: Structure of human ketohexokinase-C in complex with fructose, NO3, and osthole Authors: Gasper, W.C. / Gardner, S. / Ross, A. / Allen, K.N. / Tolan, D.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.5 KB | Display | ![]() |
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PDB format | ![]() | 55.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 804.3 KB | Display | ![]() |
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Full document | ![]() | 808 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3q92S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 34733.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Sugar | ChemComp-FRU / |
#3: Chemical | ChemComp-A0O / |
#4: Chemical | ChemComp-NO3 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.5 % |
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Crystal grow | Temperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Bis-Tris, pH 5.5, 2 M ammonium sulfate, 1.3 M potassium nitrate, 100 mM magnesium chloride, 220 mM fructose, 3.8 mM osthole |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jan 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.79 Å / Num. obs: 20332 / % possible obs: 97 % / Redundancy: 46.4 % / Biso Wilson estimate: 33.25 Å2 / CC1/2: 0.97 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1568 / CC1/2: 0.83 / % possible all: 76 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3Q92 Resolution: 2.3→47.79 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 78.55 Å2 / Biso mean: 33.252 Å2 / Biso min: 12.32 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→47.79 Å
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LS refinement shell | Resolution: 2.3001→2.3823 Å
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