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Yorodumi- PDB-6ls5: Structure of human liver FBPase complexed with covalent allosteri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ls5 | ||||||
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Title | Structure of human liver FBPase complexed with covalent allosteric inhibitor | ||||||
Components | Fructose-1,6-bisphosphatase 1Fructose 1,6-bisphosphatase | ||||||
Keywords | HYDROLASE / FBPase | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.031 Å | ||||||
Authors | Yunyuan, H. / Rongrong, S. / Yixiang, X. / Shuaishuai, N. / Yanliang, R. / Jian, L. / Jian, W. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: Identification of the New Covalent Allosteric Binding Site of Fructose-1,6-bisphosphatase with Disulfiram Derivatives toward Glucose Reduction. Authors: Huang, Y. / Xu, Y. / Song, R. / Ni, S. / Liu, J. / Xu, Y. / Ren, Y. / Rao, L. / Wang, Y. / Wei, L. / Feng, L. / Su, C. / Peng, C. / Li, J. / Wan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ls5.cif.gz | 275.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ls5.ent.gz | 218.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ls5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/6ls5 ftp://data.pdbj.org/pub/pdb/validation_reports/ls/6ls5 | HTTPS FTP |
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-Related structure data
Related structure data | 5zwkS 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: 38776.508 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FBP1, hCG_1640493 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2TU34, UniProt: P09467*PLUS #2: Chemical | ChemComp-EUF / | #3: Chemical | ChemComp-AMP / #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.64 Å3/Da / Density % sol: 53.37 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.05 M Tris (pH 6.8), 10% (v/v) polyethylene glycol 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.06 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06 Å / Relative weight: 1 |
Reflection | Resolution: 2.031→42.842 Å / Num. obs: 1353784 / % possible obs: 99.7 % / Redundancy: 8.4 % / CC1/2: 0.996 / Net I/σ(I): 11.34 |
Reflection shell | Resolution: 2.031→2.041 Å / Mean I/σ(I) obs: 2.29 / Num. unique obs: 12417 / CC1/2: 0.765 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZWK Resolution: 2.031→42.842 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.4 Å2 / Biso mean: 33.0536 Å2 / Biso min: 16.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.031→42.842 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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