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Yorodumi- PDB-4cxx: Crystal structure of human FTO in complex with acylhydrazine inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cxx | ||||||
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Title | Crystal structure of human FTO in complex with acylhydrazine inhibitor 16 | ||||||
Components | ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE FTO | ||||||
Keywords | OXIDOREDUCTASE / SMALL MOLECULAR PROBE | ||||||
Function / homology | Function and homology information regulation of white fat cell proliferation / tRNA demethylase activity / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / regulation of respiratory system process / regulation of lipid storage / regulation of brown fat cell differentiation / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity ...regulation of white fat cell proliferation / tRNA demethylase activity / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / regulation of respiratory system process / regulation of lipid storage / regulation of brown fat cell differentiation / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / snRNA processing / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / RNA repair / DNA alkylation repair / temperature homeostasis / mRNA destabilization / regulation of multicellular organism growth / adipose tissue development / ferrous iron binding / transferase activity / nuclear speck / intracellular membrane-bounded organelle / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å | ||||||
Authors | Toh, D.W. / Sun, L. / Tan, J. / Chen, Y. / Lau, L.Z.M. / Hong, W. / Woon, E.C.Y. / Gao, Y.G. | ||||||
Citation | Journal: Chem Sci / Year: 2015 Title: A strategy based on nucleotide specificity leads to a subfamily-selective and cell-active inhibitor ofN6-methyladenosine demethylase FTO. Authors: Toh, J.D.W. / Sun, L. / Lau, L.Z.M. / Tan, J. / Low, J.J.A. / Tang, C.W.Q. / Cheong, E.J.Y. / Tan, M.J.H. / Chen, Y. / Hong, W. / Gao, Y.G. / Woon, E.C.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cxx.cif.gz | 108.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cxx.ent.gz | 81.2 KB | Display | PDB format |
PDBx/mmJSON format | 4cxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cxx_validation.pdf.gz | 641.3 KB | Display | wwPDB validaton report |
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Full document | 4cxx_full_validation.pdf.gz | 661.4 KB | Display | |
Data in XML | 4cxx_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 4cxx_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/4cxx ftp://data.pdbj.org/pub/pdb/validation_reports/cx/4cxx | HTTPS FTP |
-Related structure data
Related structure data | 4cxwC 4cxyC 4ie5S 4cxz 4cy0 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: 56823.047 Da / Num. of mol.: 1 / Fragment: DEMETHYLASE, RESIDUES 32-505 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q9C0B1, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor |
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#2: Chemical | ChemComp-NI / |
#3: Chemical | ChemComp-640 / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.03 % / Description: NONE |
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Crystal grow | Temperature: 293 K Details: 100 MM SODIUM CITRATE, PH 5.6, 10% PEG 3350, 10% T-BUTANOL, 1MM NISO4, 1.5 MM LIGAND, 293 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→49.18 Å / Num. obs: 16658 / % possible obs: 99.5 % / Observed criterion σ(I): 1.91 / Redundancy: 4.04 % / Biso Wilson estimate: 85.19 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.96 |
Reflection shell | Resolution: 2.71→2.76 Å / Redundancy: 3.89 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.91 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4IE5 Resolution: 2.76→49.181 Å / SU ML: 0.49 / σ(F): 0.83 / Phase error: 35.32 / 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 mean: 90.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.76→49.181 Å
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Refine LS restraints |
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LS refinement shell |
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