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Yorodumi- PDB-5wbz: Structure of human Ketohexokinase complexed with hits from fragme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wbz | ||||||
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Title | Structure of human Ketohexokinase complexed with hits from fragment screening | ||||||
Components | Ketohexokinase | ||||||
Keywords | TRANSFERASE / Ketohexokinase / Fragment-based drug discovery / SBDD | ||||||
Function / homology | Function and homology information Essential fructosuria / ketohexokinase / ketohexokinase activity / Fructose catabolism / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose ...Essential fructosuria / ketohexokinase / ketohexokinase activity / Fructose catabolism / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å | ||||||
Authors | Pandit, J. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Discovery of Fragment-Derived Small Molecules for in Vivo Inhibition of Ketohexokinase (KHK). Authors: Huard, K. / Ahn, K. / Amor, P. / Beebe, D.A. / Borzilleri, K.A. / Chrunyk, B.A. / Coffey, S.B. / Cong, Y. / Conn, E.L. / Culp, J.S. / Dowling, M.S. / Gorgoglione, M.F. / Gutierrez, J.A. / ...Authors: Huard, K. / Ahn, K. / Amor, P. / Beebe, D.A. / Borzilleri, K.A. / Chrunyk, B.A. / Coffey, S.B. / Cong, Y. / Conn, E.L. / Culp, J.S. / Dowling, M.S. / Gorgoglione, M.F. / Gutierrez, J.A. / Knafels, J.D. / Lachapelle, E.A. / Pandit, J. / Parris, K.D. / Perez, S. / Pfefferkorn, J.A. / Price, D.A. / Raymer, B. / Ross, T.T. / Shavnya, A. / Smith, A.C. / Subashi, T.A. / Tesz, G.J. / Thuma, B.A. / Tu, M. / Weaver, J.D. / Weng, Y. / Withka, J.M. / Xing, G. / Magee, T.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wbz.cif.gz | 135.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wbz.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 5wbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/5wbz ftp://data.pdbj.org/pub/pdb/validation_reports/wb/5wbz | HTTPS FTP |
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-Related structure data
Related structure data | 5wbmC 5wboC 5wbpC 5wbqC 5wbrC 3nbvS 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: 34076.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KHK / Production host: Escherichia coli (E. coli) / References: UniProt: P50053, ketohexokinase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 17% PEG 8k, 0.1M Na-Citrate, 0.2M Ammonium sulfate, pH 4.5 Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→137.616 Å / Num. all: 39513 / Num. obs: 39513 / % possible obs: 99.6 % / Redundancy: 6 % / Biso Wilson estimate: 63.61 Å2 / Rpim(I) all: 0.034 / Rrim(I) all: 0.086 / Rsym value: 0.074 / Net I/av σ(I): 7.4 / Net I/σ(I): 14.3 / Num. measured all: 236415 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3NBV Resolution: 2.4→73.16 Å / Cor.coef. Fo:Fc: 0.9478 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.224 / SU Rfree Blow DPI: 0.179 / SU Rfree Cruickshank DPI: 0.179
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Displacement parameters | Biso max: 145.23 Å2 / Biso mean: 56.13 Å2 / Biso min: 25.33 Å2
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Refine analyze | Luzzati coordinate error obs: 0.287 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→73.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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