+Open data
-Basic information
Entry | Database: PDB / ID: 6g8f | ||||||
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Title | Crystal structure of UTX complexed with GSK-J1 | ||||||
Components | Lysine-specific demethylase 6A | ||||||
Keywords | OXIDOREDUCTASE / Jumonji Demethylase / Inhibitor | ||||||
Function / homology | Function and homology information [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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.043 Å | ||||||
Authors | Esposito, C. / Sledz, P. / Caflisch, A. | ||||||
Citation | Journal: J Chem Inf Model / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g8f.cif.gz | 120.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g8f.ent.gz | 88.5 KB | Display | PDB format |
PDBx/mmJSON format | 6g8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g8f_validation.pdf.gz | 771 KB | Display | wwPDB validaton report |
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Full document | 6g8f_full_validation.pdf.gz | 776.4 KB | Display | |
Data in XML | 6g8f_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 6g8f_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/6g8f ftp://data.pdbj.org/pub/pdb/validation_reports/g8/6g8f | HTTPS FTP |
-Related structure data
Related structure data | 6fukC 6fulC 3avsS S: Starting model for refinement C: citing same article (ref.) |
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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
-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.) Homo sapiens (human) / Gene: KDM6A, UTX / Production host: Escherichia coli BL21(DE3) (bacteria) 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, 249 molecules
#2: Chemical | ChemComp-MN / | ||||
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#3: Chemical | ChemComp-ZN / | ||||
#4: Chemical | ChemComp-K0I / | ||||
#5: Chemical | ChemComp-DMS / #6: Chemical | ChemComp-CL / | #7: 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: 2.55 Å3/Da / Density % sol: 51.75 % |
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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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→48.919 Å / Num. obs: 72632 / % possible obs: 96.1 % / Redundancy: 2 % / Net I/σ(I): 11.06 |
Reflection shell | Resolution: 2.04→6.09 Å / Redundancy: 1.91 % / Mean I/σ(I) obs: 1.37 / Num. unique obs: 11283 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AVS Resolution: 2.043→48.919 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 27.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.043→48.919 Å
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Refine LS restraints |
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LS refinement shell |
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