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Yorodumi- PDB-4ly9: Human GKRP complexed to AMG-1694 [(2R)-1,1,1-trifluoro-2-{4-[(2S)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ly9 | ||||||
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Title | Human GKRP complexed to AMG-1694 [(2R)-1,1,1-trifluoro-2-{4-[(2S)-2-{[(3S)-3-methylmorpholin-4-yl]methyl}-4-(thiophen-2-ylsulfonyl)piperazin-1-yl]phenyl}propan-2-ol] and sorbitol-6-phosphate | ||||||
Components | Glucokinase regulatory protein | ||||||
Keywords | Carbohydrate Binding protein / Regulatory protein / disruptor ligand complex / SIS domains / GKRP binds to GK / Liver | ||||||
Function / homology | Function and homology information negative regulation of glucokinase activity / fructose-6-phosphate binding / glucose sensor activity / urate metabolic process / kinase inhibitor activity / carbohydrate derivative metabolic process / response to fructose / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / triglyceride homeostasis ...negative regulation of glucokinase activity / fructose-6-phosphate binding / glucose sensor activity / urate metabolic process / kinase inhibitor activity / carbohydrate derivative metabolic process / response to fructose / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / triglyceride homeostasis / enzyme inhibitor activity / response to glucose / protein import into nucleus / glucose homeostasis / carbohydrate binding / carbohydrate metabolic process / enzyme binding / mitochondrion / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Jordan, S.R. | ||||||
Citation | Journal: Nature / Year: 2013 Title: Antidiabetic effects of glucokinase regulatory protein small-molecule disruptors. Authors: Lloyd, D.J. / St Jean, D.J. / Kurzeja, R.J. / Wahl, R.C. / Michelsen, K. / Cupples, R. / Chen, M. / Wu, J. / Sivits, G. / Helmering, J. / Komorowski, R. / Ashton, K.S. / Pennington, L.D. / ...Authors: Lloyd, D.J. / St Jean, D.J. / Kurzeja, R.J. / Wahl, R.C. / Michelsen, K. / Cupples, R. / Chen, M. / Wu, J. / Sivits, G. / Helmering, J. / Komorowski, R. / Ashton, K.S. / Pennington, L.D. / Fotsch, C. / Vazir, M. / Chen, K. / Chmait, S. / Zhang, J. / Liu, L. / Norman, M.H. / Andrews, K.L. / Bartberger, M.D. / Van, G. / Galbreath, E.J. / Vonderfecht, S.L. / Wang, M. / Jordan, S.R. / Veniant, M.M. / Hale, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ly9.cif.gz | 241 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ly9.ent.gz | 193.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ly9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/4ly9 ftp://data.pdbj.org/pub/pdb/validation_reports/ly/4ly9 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 70249.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GCKR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14397 #3: Sugar | |
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-Non-polymers , 5 types, 171 molecules
#2: Chemical | ChemComp-IOD / #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 3.01 Å3/Da / Density % sol: 59.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M bis-tris, 0.2M NaI, 16% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1 Å |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Apr 20, 2010 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→28.87 Å / Num. all: 65014 / Num. obs: 65340 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→28.87 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.907 / SU B: 7.471 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.299 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 46.277 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→28.87 Å
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