+Open data
-Basic information
Entry | Database: PDB / ID: 4op2 | ||||||
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Title | GKRP bound to AMG-0471 and Sorbitol-6-Phosphate | ||||||
Components | Glucokinase Regulatory Protein | ||||||
Keywords | CARBOHYDRATE BINDING PROTEIN/INHIBITOR / SIS domain containing protein / Binds to and inhibits Glucokinase / Glucokinase / CARBOHYDRATE BINDING PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information negative regulation of glucokinase activity / glucose sensor activity / carbohydrate derivative metabolic process / fructose-6-phosphate binding / kinase inhibitor activity / urate metabolic process / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / response to fructose / enzyme inhibitor activity ...negative regulation of glucokinase activity / glucose sensor activity / carbohydrate derivative metabolic process / fructose-6-phosphate binding / kinase inhibitor activity / urate metabolic process / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / response to fructose / enzyme inhibitor activity / triglyceride homeostasis / response to glucose / protein import into nucleus / glucose homeostasis / carbohydrate binding / enzyme binding / mitochondrion / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Jordan, S.R. / Chmait, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Small Molecule Disruptors of the Glucokinase-Glucokinase Regulatory Protein Interaction: 5. A Novel Aryl Sulfone Series, Optimization Through Conformational Analysis. Authors: Tamayo, N.A. / Norman, M.H. / Bartberger, M.D. / Hong, F.T. / Bo, Y. / Liu, L. / Nishimura, N. / Yang, K.C. / Tadesse, S. / Fotsch, C. / Chen, J. / Chmait, S. / Cupples, R. / Hale, C. / ...Authors: Tamayo, N.A. / Norman, M.H. / Bartberger, M.D. / Hong, F.T. / Bo, Y. / Liu, L. / Nishimura, N. / Yang, K.C. / Tadesse, S. / Fotsch, C. / Chen, J. / Chmait, S. / Cupples, R. / Hale, C. / Jordan, S.R. / Lloyd, D.J. / Sivits, G. / Van, G. / St Jean, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4op2.cif.gz | 243.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4op2.ent.gz | 194.4 KB | Display | PDB format |
PDBx/mmJSON format | 4op2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4op2_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4op2_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4op2_validation.xml.gz | 45.8 KB | Display | |
Data in CIF | 4op2_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/4op2 ftp://data.pdbj.org/pub/pdb/validation_reports/op/4op2 | HTTPS FTP |
-Related structure data
Related structure data | 4op1C 4op3C 4ly9S C: citing same article (ref.) S: Starting model for refinement |
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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, 4 molecules AB
#1: Protein | Mass: 70306.617 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, 211 molecules
#2: Chemical | #4: Chemical | ChemComp-IOD / #5: Chemical | ChemComp-GOL / | #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: 59.09 % |
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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 SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Apr 25, 2011 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→50 Å / Num. all: 76070 / Num. obs: 71470 / % possible obs: 93.9 % / Observed criterion σ(F): 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4LY9 Resolution: 2.24→36.32 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.057 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.228 / 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: 47.628 Å2
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Refinement step | Cycle: LAST / Resolution: 2.24→36.32 Å
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Refine LS restraints |
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