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Yorodumi- PDB-8ym7: Crystal structure of Lysine Specific Demethylase 1 (LSD1) with JH-45 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ym7 | ||||||
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Title | Crystal structure of Lysine Specific Demethylase 1 (LSD1) with JH-45 | ||||||
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Keywords | FLAVOPROTEIN / LSD1 | ||||||
Function / homology | Function and homology information positive regulation of megakaryocyte differentiation / guanine metabolic process / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / regulation of DNA methylation-dependent heterochromatin formation / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development ...positive regulation of megakaryocyte differentiation / guanine metabolic process / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / regulation of DNA methylation-dependent heterochromatin formation / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development / positive regulation of neural precursor cell proliferation / neuron maturation / regulation of androgen receptor signaling pathway / MRF binding / DNA repair complex / DNA repair-dependent chromatin remodeling / nuclear androgen receptor binding / regulation of double-strand break repair via homologous recombination / positive regulation of neuroblast proliferation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of stem cell proliferation / negative regulation of DNA binding / histone H3K9 demethylase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase complex / positive regulation of cell size / histone demethylase activity / positive regulation of epithelial to mesenchymal transition / response to fungicide / cellular response to cAMP / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription repressor complex / erythrocyte differentiation / nuclear receptor coactivator activity / negative regulation of protein binding / Regulation of PTEN gene transcription / positive regulation of protein ubiquitination / HDACs deacetylate histones / promoter-specific chromatin binding / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / negative regulation of DNA-binding transcription factor activity / cellular response to gamma radiation / cerebral cortex development / positive regulation of neuron projection development / transcription corepressor activity / cellular response to UV / regulation of protein localization / p53 binding / positive regulation of cold-induced thermogenesis / chromatin organization / flavin adenine dinucleotide binding / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription factor binding / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / Potential therapeutics for SARS / chromosome, telomeric region / transcription coactivator activity / oxidoreductase activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å | ||||||
Authors | Zhiyan, D. / Danyan, C. / Hong, J. / Tongchao, L. / Bing, X. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Discovery of Novel LSD1 Inhibitors for the Treatment of Autosomal Dominant Polycystic Kidney Disease Authors: Jiang, H. / Tongchao, L. / Bing, X. / Zhiyan, D. / Danyan, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ym7.cif.gz | 175.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ym7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ym7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/8ym7 ftp://data.pdbj.org/pub/pdb/validation_reports/ym/8ym7 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 73447.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KDM1A, AOF2, KDM1, KIAA0601, LSD1 / Production host: Escherichia coli (E. coli) References: UniProt: O60341, [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase |
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#2: Protein | Mass: 15446.615 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RCOR1, KIAA0071, RCOR / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKL0 |
#3: Chemical | ChemComp-FAD / |
#4: Chemical | ChemComp-A1LZJ / Mass: 438.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H23FN6 / Feature type: SUBJECT OF INVESTIGATION |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 7.08 Å3/Da / Density % sol: 82.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium acetate pH 4.6 1.2 M Sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979191 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 13, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979191 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→117.17 Å / Num. obs: 115950 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.995 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.83→2.98 Å / Num. unique obs: 8729 / CC1/2: 0.473 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→117.17 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.83→117.17 Å
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Refine LS restraints |
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LS refinement shell |
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