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Yorodumi- PDB-2fhy: Structure of human liver FPBase complexed with a novel benzoxazol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fhy | ||||||
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Title | Structure of human liver FPBase complexed with a novel benzoxazole as allosteric inhibitor | ||||||
Components | Fructose-1,6-bisphosphatase 1Fructose 1,6-bisphosphatase | ||||||
Keywords | HYDROLASE / allosteric inhibitors human FBPase / benzoxazole / intersubunit allosteric inhibition of human FPBase | ||||||
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 / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / Gluconeogenesis ...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 / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / Gluconeogenesis / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Abad-Zapatero, C. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: Benzoxazole benzenesulfonamides are novel allosteric inhibitors of fructose-1,6-bisphosphatase with a distinct binding mode. Authors: von Geldern, T.W. / Lai, C. / Gum, R.J. / Daly, M. / Sun, C. / Fry, E.H. / Abad-Zapatero, C. #1: Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: Benzoxazole benzenesulfonamides as allosteric inhibitors of fructose-1,6-bisphosphatase. Authors: Lai, C. / Gum, R.J. / Daly, M. / Fry, E.H. / Hutchins, C. / Abad-Zapatero, C. / von Geldern, T.W. | ||||||
History |
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Remark 600 | HETEROGEN REGARDING THE LIGAND A37, THE USER SHOULD REFER TO COMPOUND NO. 1 IN THE MAIN REFERENCE ...HETEROGEN REGARDING THE LIGAND A37, THE USER SHOULD REFER TO COMPOUND NO. 1 IN THE MAIN REFERENCE FOR THIS ENTRY, VON GELDERN ET AL. (FIG. 1). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fhy.cif.gz | 255.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fhy.ent.gz | 204.8 KB | Display | PDB format |
PDBx/mmJSON format | 2fhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/2fhy ftp://data.pdbj.org/pub/pdb/validation_reports/fh/2fhy | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Details | The biological active unit is the tetramer. Crystal contains four molecules in the asymmetric unit (A, D, H, L). They are included in the deposition |
-Components
#1: Protein | Mass: 40994.887 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: 6His-Xpress-huFBP1-pET100-D-TOPO / Production host: Escherichia coli (E. coli) References: GenBank: 15277851, UniProt: P09467*PLUS, fructose-bisphosphatase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-A37 / |
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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: 2.66 Å3/Da / Density % sol: 53.72 % |
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Crystal grow | Method: vapor diffusion, under oil / pH: 6.5 Details: 0.2 M magnesium acetate, 0.1M sodium cacodylate, 20% PEG8K in the presence of ZMP, pH 6.5, vapor diffusion, under oil |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 22, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.95→20 Å / Num. all: 33966 / Num. obs: 32415 / % possible obs: 88.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.95→3.04 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2467 / Rsym value: 0.238 / % possible all: 65.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→19.89 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 410349.17 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: Entries 2fhy, 2fie and 2fix characterize the binding mode of benzoxazoles as allosteric inhibitors of human liver FBPase as described in the associated references. These three entries focus ...Details: Entries 2fhy, 2fie and 2fix characterize the binding mode of benzoxazoles as allosteric inhibitors of human liver FBPase as described in the associated references. These three entries focus on the binding mode and interactions in the proximity of the ligands. The medium to low resolution of the crystallographic data (3.3, 2.95 and 2.8 A) and the limited quality and extent of the available data, especially for entry 2fix, should be considered when trying to extract accurate interatomic distances between the ligands and the protein, at certain regions of the protein exposed to solvent.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.8 Å2 / ksol: 0.303437 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.95→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.06 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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