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- PDB-6ful: Crystal structure of UTX complexed with 5-hydroxy-4-keto-1-methyl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ful | ||||||
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Title | Crystal structure of UTX complexed with 5-hydroxy-4-keto-1-methyl-picolinate | ||||||
![]() | Lysine-specific demethylase 6A | ||||||
![]() | OXIDOREDUCTASE / Jumonji Demethylase / Inhibitor | ||||||
Function / homology | ![]() [histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / MLL3/4 complex / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / histone demethylase activity / Chromatin modifications during the maternal to zygotic transition (MZT) / HDMs demethylate histones / chromatin DNA binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis ...[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / MLL3/4 complex / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / histone demethylase activity / Chromatin modifications during the maternal to zygotic transition (MZT) / HDMs demethylate histones / chromatin DNA binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / heart development / regulation of gene expression / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Esposito, C. / Sledz, P. / Caflisch, A. | ||||||
![]() | ![]() Title: In Silico Identification of JMJD3 Demethylase Inhibitors. Authors: Esposito, C. / Wiedmer, L. / Caflisch, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.3 KB | Display | ![]() |
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PDB format | ![]() | 97.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.7 KB | Display | ![]() |
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Full document | ![]() | 467.7 KB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 40.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fukC ![]() 6g8fC ![]() 3avsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60264.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O15550, 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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-Non-polymers , 6 types, 637 molecules ![](data/chem/img/E7Z.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PG0.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PG0.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-E7Z / | ||||
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#3: Chemical | ChemComp-MN / | ||||
#4: Chemical | ChemComp-ZN / | ||||
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-PG0 / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-HCl (pH 8.5), Li2 SO4 (0.15-0.25 M), PEG 3350 (20-25% w/v) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.649→48.761 Å / Num. obs: 138199 / % possible obs: 96.9 % / Redundancy: 1.96 % / Net I/σ(I): 8.02 |
Reflection shell | Resolution: 1.649→4.92 Å / Redundancy: 1.9 % / Num. unique obs: 22076 / % possible all: 95.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3AVS Resolution: 1.649→48.761 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 22.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.649→48.761 Å
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Refine LS restraints |
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LS refinement shell |
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