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Yorodumi- PDB-5vmp: Crystal Structure of Human KDM4 with Small Molecule Inhibitor QC5714 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vmp | ||||||
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Title | Crystal Structure of Human KDM4 with Small Molecule Inhibitor QC5714 | ||||||
Components | Lysine-specific demethylase 4A | ||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / KDM4 / 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 / 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: 2.48 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 | 5vmp.cif.gz | 296 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vmp.ent.gz | 239.1 KB | Display | PDB format |
PDBx/mmJSON format | 5vmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vmp_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5vmp_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5vmp_validation.xml.gz | 50.1 KB | Display | |
Data in CIF | 5vmp_validation.cif.gz | 69.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/5vmp ftp://data.pdbj.org/pub/pdb/validation_reports/vm/5vmp | HTTPS FTP |
-Related structure data
Related structure data | 5vgiC 3pdqS 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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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 42975.770 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-9FJ / #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: 2.57 Å3/Da / Density % sol: 52.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 22% PEG4K, 100mM HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / 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: 2.48→50 Å / Num. obs: 57177 / % possible obs: 99 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.127 / Χ2: 1.035 / Net I/σ(I): 5.7 / Num. measured all: 214006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PDQ Resolution: 2.48→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.2598 / WRfactor Rwork: 0.1914 / FOM work R set: 0.7918 / SU B: 10.99 / SU ML: 0.239 / SU R Cruickshank DPI: 0.5994 / SU Rfree: 0.305 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.599 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.86 Å2 / Biso mean: 41.597 Å2 / Biso min: 13.69 Å2
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Refinement step | Cycle: final / Resolution: 2.48→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.481→2.545 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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