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- PDB-3nc9: X-ray structure of ketohexokinase complexed with an indazole compound -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nc9 | ||||||
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Title | X-ray structure of ketohexokinase complexed with an indazole compound | ||||||
![]() | Ketohexokinase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / ketohexokinase / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Abad, M.C. / Gibbs, A.C. / Spurlino, J.C. | ||||||
![]() | ![]() Title: Electron density guided fragment-based lead discovery of ketohexokinase inhibitors. Authors: Gibbs, A.C. / Abad, M.C. / Zhang, X. / Tounge, B.A. / Lewandowski, F.A. / Struble, G.T. / Sun, W. / Sui, Z. / Kuo, L.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128 KB | Display | ![]() |
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PDB format | ![]() | 99 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 23.8 KB | Display | |
Data in CIF | ![]() | 32.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3nbvSC ![]() 3nbwC ![]() 3nc2C ![]() 3ncaC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34076.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P50053-2, UniProt: P50053*PLUS, ketohexokinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.42 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 17% PEG8k, 0.1M Na-Citrate, 0.2M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 3, 2009 / Details: mirrors |
Radiation | Monochromator: double crystal mono, Si(111) from accel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→44.9 Å / Num. all: 38770 / Num. obs: 38469 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.64 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.64 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 3856 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3NBV Resolution: 2.4→36.314 Å / SU ML: 0.43 / Isotropic thermal model: anisotropic / σ(F): 0.04 / σ(I): 0 / 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 / Bsol: 64.121 Å2 / ksol: 0.389 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→36.314 Å
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Refine LS restraints |
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LS refinement shell |
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