+Open data
-Basic information
Entry | Database: PDB / ID: 6w0w | ||||||
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Title | Structure of KHK in complex with compound 3 | ||||||
Components | Ketohexokinase | ||||||
Keywords | TRANSFERASE / Ketohexokinase | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Jasti, J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Discovery of PF-06835919: A Potent Inhibitor of Ketohexokinase (KHK) for the Treatment of Metabolic Disorders Driven by the Overconsumption of Fructose. Authors: Futatsugi, K. / Smith, A.C. / Tu, M. / Raymer, B. / Ahn, K. / Coffey, S.B. / Dowling, M.S. / Fernando, D.P. / Gutierrez, J.A. / Huard, K. / Jasti, J. / Kalgutkar, A.S. / Knafels, J.D. / ...Authors: Futatsugi, K. / Smith, A.C. / Tu, M. / Raymer, B. / Ahn, K. / Coffey, S.B. / Dowling, M.S. / Fernando, D.P. / Gutierrez, J.A. / Huard, K. / Jasti, J. / Kalgutkar, A.S. / Knafels, J.D. / Pandit, J. / Parris, K.D. / Perez, S. / Pfefferkorn, J.A. / Price, D.A. / Ryder, T. / Shavnya, A. / Stock, I.A. / Tsai, A.S. / Tesz, G.J. / Thuma, B.A. / Weng, Y. / Wisniewska, H.M. / Xing, G. / Zhou, J. / 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 | 6w0w.cif.gz | 249.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w0w.ent.gz | 201.7 KB | Display | PDB format |
PDBx/mmJSON format | 6w0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w0w_validation.pdf.gz | 404.5 KB | Display | wwPDB validaton report |
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Full document | 6w0w_full_validation.pdf.gz | 404.5 KB | Display | |
Data in XML | 6w0w_validation.xml.gz | 1.4 KB | Display | |
Data in CIF | 6w0w_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/6w0w ftp://data.pdbj.org/pub/pdb/validation_reports/w0/6w0w | HTTPS FTP |
-Related structure data
Related structure data | 6w0nC 6w0xC 6w0yC 6w0zC 5wbmS 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 | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 66.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 17-20% PEG 8000, 100 mM sodium citrate, pH 4.4-4.7, and 0.2 M ammonium sulfate PH range: 4.4-4.7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→71.45 Å / Num. obs: 24722 / % possible obs: 98.2 % / Redundancy: 6.2 % / CC1/2: 0.999 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 2.8→2.95 Å / Num. unique obs: 3164 / CC1/2: 0.888 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5wbm Resolution: 2.8→31.42 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.448 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.445 / SU Rfree Blow DPI: 0.261 / SU Rfree Cruickshank DPI: 0.264
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Displacement parameters | Biso max: 198.16 Å2 / Biso mean: 89.69 Å2 / Biso min: 36.25 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→31.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.83 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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