+Open data
-Basic information
Entry | Database: PDB / ID: 6kgk | ||||||
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Title | LSD1-CoREST-S2101 five-membered ring adduct model | ||||||
Components |
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Keywords | OXIDOREDUCTASE / DEMETHYLASE / AMINE OXIDASE / CHROMATIN / HISTONE / FAD / MECHANISM-BASED INHIBITOR | ||||||
Function / homology | Function and homology information positive regulation of megakaryocyte differentiation / guanine metabolic process / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / protein demethylation / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / regulation of DNA methylation-dependent heterochromatin formation / muscle cell development / histone H3K4 demethylase activity ...positive regulation of megakaryocyte differentiation / guanine metabolic process / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / protein demethylation / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / regulation of DNA methylation-dependent heterochromatin formation / muscle cell development / histone H3K4 demethylase activity / positive regulation of neural precursor cell proliferation / neuron maturation / MRF binding / regulation of androgen receptor signaling pathway / 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 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to fungicide / cellular response to cAMP / transcription repressor complex / erythrocyte differentiation / nuclear receptor coactivator activity / negative regulation of protein binding / Regulation of PTEN gene transcription / positive regulation of protein ubiquitination / promoter-specific chromatin binding / HDACs deacetylate histones / cellular response to gamma radiation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / negative regulation of DNA-binding transcription factor activity / positive regulation of neuron projection development / cerebral cortex development / transcription corepressor activity / cellular response to UV / regulation of protein localization / p53 binding / flavin adenine dinucleotide binding / chromatin organization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / 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 / 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: 2.7 Å | ||||||
Authors | Niwa, H. / Sato, S. / Sengoku, S. / Umehara, T. / Yokoyama, S. | ||||||
Citation | Journal: Chemmedchem / Year: 2020 Title: Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors. Authors: Niwa, H. / Sato, S. / Handa, N. / Sengoku, T. / Umehara, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kgk.cif.gz | 339.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kgk.ent.gz | 275.5 KB | Display | PDB format |
PDBx/mmJSON format | 6kgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/6kgk ftp://data.pdbj.org/pub/pdb/validation_reports/kg/6kgk | HTTPS FTP |
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-Related structure data
Related structure data | 6kglC 6kgmC 6kgnC 6kgoC 6kgpC 6kgqC 6kgrC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 74333.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. / Source: (gene. exp.) Homo sapiens (human) / Gene: KDM1A, AOF2, KDM1, KIAA0601, LSD1 / Plasmid: PLASMID / Details (production host): PETDUET-1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3) / References: UniProt: O60341, Oxidoreductases |
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#2: Protein | Mass: 15850.929 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. / Source: (gene. exp.) Homo sapiens (human) / Gene: RCOR1, KIAA0071, RCOR / Production host: Escherichia coli KRX (bacteria) / Strain (production host): KRX / References: UniProt: Q9UKL0 |
-Non-polymers , 4 types, 58 molecules
#3: Chemical | #4: Chemical | ChemComp-DJ0 / | #5: Chemical | ChemComp-FAD / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Nonpolymer details | 6KGK and 6KGL use the same data but have ligand models with possible different configurations. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.93 Å3/Da / Density % sol: 82.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M N-(carbamoylmethyl)iminodiacetic acid (pH 5.5), 1.23 M potassium sodium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Feb 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→49 Å / Num. obs: 68943 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 70.4 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.027 / Rrim(I) all: 0.074 / Rsym value: 0.069 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.7→2.76 Å / Redundancy: 7.6 % / Num. unique obs: 4590 / CC1/2: 0.79 / Rpim(I) all: 0.482 / Rrim(I) all: 1.341 / Rsym value: 1.25 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→48.96 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 24.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→48.96 Å
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Refine LS restraints |
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LS refinement shell |
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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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