+Open data
-Basic information
Entry | Database: PDB / ID: 8fj4 | ||||||
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Title | LSD1-CoREST in complex with T108, short soaking | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Epigenetics / Histone demethylase / Drug resistance / Covalent inhibitor | ||||||
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 / 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 / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development / neuron maturation / positive regulation of neural precursor cell proliferation / 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 / positive regulation of protein ubiquitination / Regulation of PTEN gene transcription / HDACs deacetylate histones / promoter-specific chromatin binding / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / negative regulation of DNA-binding transcription factor activity / HDMs demethylate histones / cellular response to gamma radiation / cerebral cortex development / positive regulation of neuron projection development / transcription corepressor activity / cellular response to UV / positive regulation of cold-induced thermogenesis / p53 binding / flavin adenine dinucleotide binding / chromatin organization / regulation of protein localization / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription regulator complex / Potential therapeutics for SARS / chromosome, telomeric region / transcription coactivator activity / oxidoreductase activity / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / enzyme binding / 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: 2.76 Å | ||||||
Authors | Caroli, J. / Mattevi, A. | ||||||
Funding support | Italy, 1items
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Citation | Journal: to be published Title: Distal drug resistance mutations promote covalent inhibitor-adduct Grob fragmentation in LSD1 Authors: Caroli, J. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fj4.cif.gz | 180.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fj4.ent.gz | 136.7 KB | Display | PDB format |
PDBx/mmJSON format | 8fj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fj4_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8fj4_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8fj4_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 8fj4_validation.cif.gz | 44.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/8fj4 ftp://data.pdbj.org/pub/pdb/validation_reports/fj/8fj4 | HTTPS FTP |
-Related structure data
Related structure data | 8bopC 8boxC 8f2zC 8f30C 8f59C 8f6sC 8fdvC 8fj6C 8fj7C 8fqjC 8friC 8frqC 8frvC 8fskC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 95051.633 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: 16459.742 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 | Mass: 306.401 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H22N2O / Feature type: SUBJECT OF INVESTIGATION #4: Chemical | ChemComp-XZQ / [( | Mass: 1038.846 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H48N10O17P2 / 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: 5.54 Å3/Da / Density % sol: 77.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.2 Na/K Tartrate, 100 mM ADA pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96546 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96546 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→48.78 Å / Num. obs: 63077 / % possible obs: 99 % / Redundancy: 4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.065 / Rrim(I) all: 0.134 / Χ2: 0.99 / Net I/σ(I): 8.3 / Num. measured all: 251831 |
Reflection shell | Resolution: 2.76→2.83 Å / % possible obs: 91.3 % / Redundancy: 4 % / Rmerge(I) obs: 2.626 / Num. measured all: 16362 / Num. unique obs: 4079 / CC1/2: 0.202 / Rpim(I) all: 1.453 / Rrim(I) all: 3.019 / Χ2: 0.96 / Net I/σ(I) obs: 0.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→48.78 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / 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: 2.76→48.78 Å
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Refine LS restraints |
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LS refinement shell |
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