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Yorodumi- PDB-5vgi: Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vgi | ||||||
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Title | Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352 | ||||||
Components | Lysine-specific demethylase 4A | ||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / KDM4 / Protein-Inhibitor Complex / demethylase / epigenetics / 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 / negative regulation of autophagy / response to nutrient levels / 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 / chromatin / positive regulation of gene expression / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Hosfield, D.J. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2017 Title: Design of KDM4 Inhibitors with Antiproliferative Effects in Cancer Models. Authors: Chen, Y.K. / Bonaldi, T. / Cuomo, A. / Del Rosario, J.R. / Hosfield, D.J. / Kanouni, T. / Kao, S.C. / Lai, C. / Lobo, N.A. / Matuszkiewicz, J. / McGeehan, A. / O'Connell, S.M. / Shi, L. / ...Authors: Chen, Y.K. / Bonaldi, T. / Cuomo, A. / Del Rosario, J.R. / Hosfield, D.J. / Kanouni, T. / Kao, S.C. / Lai, C. / Lobo, N.A. / Matuszkiewicz, J. / McGeehan, A. / O'Connell, S.M. / Shi, L. / Stafford, J.A. / Stansfield, R.K. / Veal, J.M. / Weiss, M.S. / Yuen, N.Y. / Wallace, M.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vgi.cif.gz | 570 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vgi.ent.gz | 469.2 KB | Display | PDB format |
PDBx/mmJSON format | 5vgi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/5vgi ftp://data.pdbj.org/pub/pdb/validation_reports/vg/5vgi | HTTPS FTP |
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-Related structure data
Related structure data | 5vmpC 5vgk 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: 43137.957 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 (E. coli) 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-9DJ / #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: 273 K / Method: vapor diffusion / Details: 25% PEG 4000, 100mM HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.08→50 Å / Num. obs: 85582 / % possible obs: 88.4 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.046 / Rrim(I) all: 0.07 / Χ2: 1.028 / Net I/σ(I): 8 / Num. measured all: 163174 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2486 / WRfactor Rwork: 0.1888 / FOM work R set: 0.7913 / SU B: 11.848 / SU ML: 0.15 / SU R Cruickshank DPI: 0.2409 / SU Rfree: 0.2071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.33 Å2 / Biso mean: 37.281 Å2 / Biso min: 16.63 Å2
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Refinement step | Cycle: final / Resolution: 2.07→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.072→2.126 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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