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Yorodumi- PDB-3kbz: Crystal structure of human liver FBPase in complex with tricyclic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kbz | ||||||
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Title | Crystal structure of human liver FBPase in complex with tricyclic inhibitor 6 | ||||||
Components | Fructose-1,6-bisphosphatase 1Fructose 1,6-bisphosphatase | ||||||
Keywords | HYDROLASE / Allosteric enzyme / Carbohydrate metabolism / Disease mutation / Gluconeogenesis / Magnesium / Metal-binding / Polymorphism | ||||||
Function / homology | Function and homology information cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process ...cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process / fructose metabolic process / Gluconeogenesis / monosaccharide binding / negative regulation of glycolytic process / cellular hyperosmotic salinity response / regulation of gluconeogenesis / AMP binding / dephosphorylation / cellular response to cAMP / response to nutrient levels / gluconeogenesis / negative regulation of cell growth / cellular response to insulin stimulus / cellular response to xenobiotic stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Takahashi, M. / Sone, J. / Hanzawa, H. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: Structure-based drug design of tricyclic 8H-indeno[1,2-d][1,3]thiazoles as potent FBPase inhibitors. Authors: Tsukada, T. / Takahashi, M. / Takemoto, T. / Kanno, O. / Yamane, T. / Kawamura, S. / Nishi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kbz.cif.gz | 251.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kbz.ent.gz | 203.5 KB | Display | PDB format |
PDBx/mmJSON format | 3kbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/3kbz ftp://data.pdbj.org/pub/pdb/validation_reports/kb/3kbz | HTTPS FTP |
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-Related structure data
Related structure data | 3kc0C 3kc1C 1ftaS 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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Unit cell |
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-Components
#1: Protein | Mass: 36728.227 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FBP1, FBP / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09467, fructose-bisphosphatase #2: Chemical | ChemComp-2T4 / {[( #3: 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: 2.65 Å3/Da / Density % sol: 53.67 % / Mosaicity: 0.555 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 8-10% PEG 3350, 0.15M NaCl, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.542 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 19, 2005 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.45→40 Å / Num. obs: 52622 / % possible obs: 89.3 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.072 / Χ2: 1.86 / Net I/σ(I): 30.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FTA Resolution: 2.45→19.86 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 1078829 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.795 Å2 / ksol: 0.367 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.73 Å2 / Biso mean: 30.8 Å2 / Biso min: 11.13 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.45→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.6 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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