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Yorodumi- PDB-6q3x: Structure of human galactokinase in complex with galactose and 2'... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q3x | ||||||
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Title | Structure of human galactokinase in complex with galactose and 2'-(benzo[d]oxazol-2-ylamino)-7',8'-dihydro-1'H-spiro[cyclohexane-1,4'-quinazolin]-5'(6'H)-one | ||||||
Components | Galactokinase | ||||||
Keywords | TRANSFERASE / GHMP Kinase / Galactose metabolism / Inhibitor / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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: 2.1 Å | ||||||
Authors | Bezerra, G.A. / Mackinnon, S. / Zhang, M. / Foster, W. / Bailey, H. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Lai, K. / Yue, W.W. / Structural Genomics Consortium (SGC) | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2021 Title: Fragment Screening Reveals Starting Points for Rational Design of Galactokinase 1 Inhibitors to Treat Classic Galactosemia. Authors: Mackinnon, S.R. / Krojer, T. / Foster, W.R. / Diaz-Saez, L. / Tang, M. / Huber, K.V.M. / von Delft, F. / Lai, K. / Brennan, P.E. / Arruda Bezerra, G. / Yue, W.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q3x.cif.gz | 163.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q3x.ent.gz | 128.8 KB | Display | PDB format |
PDBx/mmJSON format | 6q3x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/6q3x ftp://data.pdbj.org/pub/pdb/validation_reports/q3/6q3x | HTTPS FTP |
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-Related structure data
Related structure data | 6zfhC 6zgvC 6zgwC 6zgxC 6zgyC 6zgzC 6zh0C 6gr2S 6q3h 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
#1: Protein | Mass: 42348.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GALK1, GALK / Production host: Escherichia coli (E. coli) / References: UniProt: P51570, galactokinase #2: Sugar | #3: Chemical | ChemComp-MPD / ( #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: 2.78 Å3/Da / Density % sol: 55.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion Details: 0.02M Sodium formate; 0.02M Ammonium acetate; 0.02M Sodium citrate tribasic dihydrate; 0.02M Sodium potassium tartrate tetrahydrate; 0.02M Sodium oxamate 0.1 M pH 7.5, Sodium HEPES; MOPS ...Details: 0.02M Sodium formate; 0.02M Ammonium acetate; 0.02M Sodium citrate tribasic dihydrate; 0.02M Sodium potassium tartrate tetrahydrate; 0.02M Sodium oxamate 0.1 M pH 7.5, Sodium HEPES; MOPS (acid) pH 7.5 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2018 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.83→57.84 Å / Num. obs: 73959 / % possible obs: 89.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 30.29 Å2 / Rpim(I) all: 0.034 / Rrim(I) all: 0.087 / Net I/σ(I): 11.5 / Num. measured all: 421459 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GR2 Resolution: 2.1→57.84 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.77 Å2 / Biso mean: 31.5728 Å2 / Biso min: 12.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→57.84 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
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