+Open data
-Basic information
Entry | Database: PDB / ID: 6h0z | ||||||
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Title | Crystal Structure of KDM4D with tetrazolylhydrazide ligand NR067 | ||||||
Components | Lysine-specific demethylase 4D | ||||||
Keywords | OXIDOREDUCTASE / KDM4D / ligand binding / Tetrazolylhydrazide / tetrazole / inhibitor design / cancer / epigenetics | ||||||
Function / homology | Function and homology information positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / regulation of protein phosphorylation / double-strand break repair via homologous recombination ...positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / regulation of protein phosphorylation / double-strand break repair via homologous recombination / HDMs demethylate histones / chromatin DNA binding / site of double-strand break / regulation of gene expression / blood microparticle / damaged DNA binding / inflammatory response / chromatin remodeling / chromatin / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||
Authors | Malecki, P.H. / Weiss, M.S. / Heinemann, U. / Link, A. | ||||||
Citation | Journal: To be published Title: Crystal Structure of KDM4D with tetrazolylhydrazide ligand NR067 Authors: Malecki, P.H. / Weiss, M.S. / Heinemann, U. / Link, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h0z.cif.gz | 186.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h0z.ent.gz | 146.1 KB | Display | PDB format |
PDBx/mmJSON format | 6h0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h0z_validation.pdf.gz | 975.6 KB | Display | wwPDB validaton report |
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Full document | 6h0z_full_validation.pdf.gz | 978.5 KB | Display | |
Data in XML | 6h0z_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 6h0z_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/6h0z ftp://data.pdbj.org/pub/pdb/validation_reports/h0/6h0z | HTTPS FTP |
-Related structure data
Related structure data | 6etsS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39491.793 Da / Num. of mol.: 1 / Fragment: JMJD2D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4D, JHDM3D, JMJD2D / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q6B0I6, 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 , 8 types, 478 molecules
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | ChemComp-CL / | ||||||||
#4: Chemical | ChemComp-NA / | ||||||||
#5: Chemical | ChemComp-EDO / #6: Chemical | #7: Chemical | ChemComp-NI / | #8: Chemical | #9: 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: 2.56 Å3/Da / Density % sol: 51.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 100mM HEPES, 180mM ammonium sulphate, 24% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.34→48.191 Å / Num. obs: 169112 / % possible obs: 99.4 % / Redundancy: 6.794 % / Biso Wilson estimate: 12.75 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.073 / Χ2: 1.279 / Net I/σ(I): 18.42 / Num. measured all: 1148877 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ETS Resolution: 1.34→42.193 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 14.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.91 Å2 / Biso mean: 19.3596 Å2 / Biso min: 7.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.34→42.193 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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