+Open data
-Basic information
Entry | Database: PDB / ID: 6cg2 | ||||||
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Title | Crystal Structure of KDM4A with Compound 8 | ||||||
Components | Lysine-specific demethylase 4A | ||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / KDM4A / Small Molecule Inhibitor / Demethylase / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information [histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / positive regulation of neuron differentiation / response to nutrient levels / negative regulation of autophagy / HDMs demethylate histones / fibrillar center / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | ||||||
Authors | Hosfield, D.J. / Nie, Z. | ||||||
Citation | Journal: Bioorg. Med. Chem. Lett. / Year: 2018 Title: Structure-based design and discovery of potent and selective KDM5 inhibitors. Authors: Nie, Z. / Shi, L. / Lai, C. / O'Connell, S.M. / Xu, J. / Stansfield, R.K. / Hosfield, D.J. / Veal, J.M. / Stafford, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cg2.cif.gz | 302.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cg2.ent.gz | 243.7 KB | Display | PDB format |
PDBx/mmJSON format | 6cg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cg2_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6cg2_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6cg2_validation.xml.gz | 54.8 KB | Display | |
Data in CIF | 6cg2_validation.cif.gz | 76.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/6cg2 ftp://data.pdbj.org/pub/pdb/validation_reports/cg/6cg2 | HTTPS FTP |
-Related structure data
Related structure data | 6cg1C 5vgiS 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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Unit cell |
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-Components
#1: Protein | Mass: 40761.441 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 / Production host: Escherichia coli K-12 (bacteria) References: UniProt: O75164, 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 #2: Chemical | ChemComp-NI / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-QC2 / #5: Water | ChemComp-HOH / | |
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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: 2.52 Å3/Da / Density % sol: 51.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG4K, 150mM NaCl, 50mM HEPES pH 7.3 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.95 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→140.33 Å / Num. obs: 67709 / % possible obs: 98.7 % / Redundancy: 3.8 % / Rsym value: 0.102 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.34→2.48 Å / Num. measured obs: 39925 / Rsym value: 0.755 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VGI Resolution: 2.34→140.3 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.307 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.35 / ESU R Free: 0.24 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 162.12 Å2 / Biso mean: 43.884 Å2 / Biso min: 16.82 Å2
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Refinement step | Cycle: final / Resolution: 2.34→140.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.336→2.396 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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