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Yorodumi- PDB-4uvb: LSD1(KDM1A)-CoREST in complex with 1-Methyl-Tranylcypromine (1S,2R) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uvb | ||||||
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Title | LSD1(KDM1A)-CoREST in complex with 1-Methyl-Tranylcypromine (1S,2R) | ||||||
Components |
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Keywords | TRANSCRIPTION / 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: 2.8 Å | ||||||
Authors | Vianello, P. / Botrugno, O. / Cappa, A. / Ciossani, G. / Dessanti, P. / Mai, A. / Mattevi, A. / Meroni, G. / Minucci, S. / Thaler, F. ...Vianello, P. / Botrugno, O. / Cappa, A. / Ciossani, G. / Dessanti, P. / Mai, A. / Mattevi, A. / Meroni, G. / Minucci, S. / Thaler, F. / Tortorici, M. / Trifiro, P. / Valente, S. / Villa, M. / Varasi, M. / Mercurio, C. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2014 Title: Synthesis, Biological Activity and Mechanistic Insights of 1-Substituted Cyclopropylamine Derivatives: A Novel Class of Irreversible Inhibitors of Histone Demethylase Kdm1A. Authors: Vianello, P. / Botrugno, O.A. / Cappa, A. / Ciossani, G. / Dessanti, P. / Mai, A. / Mattevi, A. / Meroni, G. / Minucci, S. / Thaler, F. / Tortorici, M. / Trifiro, P. / Valente, S. / Villa, M. ...Authors: Vianello, P. / Botrugno, O.A. / Cappa, A. / Ciossani, G. / Dessanti, P. / Mai, A. / Mattevi, A. / Meroni, G. / Minucci, S. / Thaler, F. / Tortorici, M. / Trifiro, P. / Valente, S. / Villa, M. / Varasi, M. / Mercurio, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uvb.cif.gz | 182.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uvb.ent.gz | 136.7 KB | Display | PDB format |
PDBx/mmJSON format | 4uvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uvb_validation.pdf.gz | 759.5 KB | Display | wwPDB validaton report |
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Full document | 4uvb_full_validation.pdf.gz | 765.1 KB | Display | |
Data in XML | 4uvb_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 4uvb_validation.cif.gz | 38.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/4uvb ftp://data.pdbj.org/pub/pdb/validation_reports/uv/4uvb | HTTPS FTP |
-Related structure data
Related structure data | 4uv8C 4uv9C 4uvaC 4uvcC 2v1dS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 94846.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: O60341, Oxidoreductases |
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#2: Protein | Mass: 53101.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: Q9UKL0 |
#3: Chemical | ChemComp-D51 / [( |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.25 Å3/Da / Density % sol: 75 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→60 Å / Num. obs: 62197 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V1D Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.144 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. 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 mean: 83.932 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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