+Open data
-Basic information
Entry | Database: PDB / ID: 7rcl | ||||||
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Title | Crystal Structure of ADP-bound Galactokinase | ||||||
Components | Galactokinase | ||||||
Keywords | SUGAR BINDING PROTEIN / GALK / galactokinase / Galactose / ADP / disulfide | ||||||
Function / homology | Function and homology information glycolytic process from galactose / Defective GALK1 causes GALCT2 / galactitol metabolic process / galactokinase / galactokinase activity / galactose catabolic process / Galactose catabolism / galactose catabolic process via UDP-galactose / galactose binding / galactose metabolic process ...glycolytic process from galactose / Defective GALK1 causes GALCT2 / galactitol metabolic process / galactokinase / galactokinase activity / galactose catabolic process / Galactose catabolism / galactose catabolic process via UDP-galactose / galactose binding / galactose metabolic process / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Model details | Human Galactokinase enzyme with ADP bound | ||||||
Authors | Whitby, F.G. / Hall, M.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2021 Title: Structure-Based Optimization of Small Molecule Human Galactokinase Inhibitors. Authors: Liu, L. / Tang, M. / Pragani, R. / Whitby, F.G. / Zhang, Y.Q. / Balakrishnan, B. / Fang, Y. / Karavadhi, S. / Tao, D. / LeClair, C.A. / Hall, M.D. / Marugan, J.J. / Boxer, M. / Shen, M. / ...Authors: Liu, L. / Tang, M. / Pragani, R. / Whitby, F.G. / Zhang, Y.Q. / Balakrishnan, B. / Fang, Y. / Karavadhi, S. / Tao, D. / LeClair, C.A. / Hall, M.D. / Marugan, J.J. / Boxer, M. / Shen, M. / Hill, C.P. / Lai, K. / Patnaik, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rcl.cif.gz | 614.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rcl.ent.gz | 509.7 KB | Display | PDB format |
PDBx/mmJSON format | 7rcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/7rcl ftp://data.pdbj.org/pub/pdb/validation_reports/rc/7rcl | HTTPS FTP |
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-Related structure data
Related structure data | 7rcmC 7s49C 7s4cC 1wuuS 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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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 42203.020 Da / Num. of mol.: 4 / Mutation: K252A, E253A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GALK1, GALK / Plasmid: pET21D / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: P51570, galactokinase #2: Sugar | ChemComp-GLA / |
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-Non-polymers , 5 types, 420 molecules
#3: Chemical | ChemComp-ADP / #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-NA / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.39 Å3/Da / Density % sol: 63.67 % / Mosaicity: 0.518 ° / Mosaicity esd: 0.006 ° |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: Seeding into drops containing GALK protein at 8 mg/ml, 2.3M Na/K pH6.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1533 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 1 / Detector: CCD / Date: Nov 21, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1533 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 86404 / % possible obs: 95.7 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.225 / Rpim(I) all: 0.069 / Rrim(I) all: 0.222 / Χ2: 1.216 / Net I/σ(I): 9 / Num. measured all: 955737 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1wuu Resolution: 2.4→39.63 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 16.248 / SU ML: 0.178 / SU R Cruickshank DPI: 0.2564 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 153.74 Å2 / Biso mean: 56.893 Å2 / Biso min: 30.76 Å2
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Refinement step | Cycle: final / Resolution: 2.4→39.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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