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Yorodumi- PDB-7cdd: Crystal structure of LSD1-CoREST in complex with PRSFLVRR peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cdd | ||||||
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Title | Crystal structure of LSD1-CoREST in complex with PRSFLVRR peptide | ||||||
Components |
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Keywords | OXIDOREDUCTASE/TRANSCRIPTION / DEMETHYLASE / AMINE OXIDASE / CHROMATIN / HISTONE / FAD / COREPRESSOR / OXIDOREDUCTASE-TRANSCRIPTION-INHIBITOR complex / OXIDOREDUCTASE / OXIDOREDUCTASE-TRANSCRIPTION complex | ||||||
Function / homology | Function and homology information positive regulation of megakaryocyte differentiation / guanine metabolic process / regulation of DNA methylation-dependent heterochromatin formation / 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 / regulation of DNA methylation-dependent heterochromatin formation / 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 / cellular response to cAMP / response to fungicide / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Regulation of PTEN gene transcription / transcription repressor complex / erythrocyte differentiation / nuclear receptor coactivator activity / positive regulation of protein ubiquitination / negative regulation of protein binding / HDACs deacetylate histones / promoter-specific chromatin binding / HDMs demethylate histones / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / negative regulation of DNA-binding transcription factor activity / p53 binding / cellular response to gamma radiation / cerebral cortex development / positive regulation of neuron projection development / transcription corepressor activity / regulation of protein localization / cellular response to UV / Factors involved in megakaryocyte development and platelet production / chromatin organization / positive regulation of cold-induced thermogenesis / flavin adenine dinucleotide binding / chromosome, telomeric region / DNA-binding transcription factor binding / Potential therapeutics for SARS / transcription regulator complex / Estrogen-dependent gene expression / transcription coactivator activity / RNA polymerase II-specific DNA-binding transcription factor binding / oxidoreductase activity / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / 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: 2.76 Å | ||||||
Authors | Kikuchi, M. / Kitagawa, H. / Sato, S. / Umezawa, N. / Higuchi, T. / Umehara, T. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Structure-Based Identification of Potent Lysine-Specific Demethylase 1 Inhibitor Peptides and Temporary Cyclization to Enhance Proteolytic Stability and Cell Growth-Inhibitory Activity. Authors: Kitagawa, H. / Kikuchi, M. / Sato, S. / Watanabe, H. / Umezawa, N. / Kato, M. / Hisamatsu, Y. / Umehara, T. / Higuchi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cdd.cif.gz | 178.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cdd.ent.gz | 134.8 KB | Display | PDB format |
PDBx/mmJSON format | 7cdd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cdd_validation.pdf.gz | 766.7 KB | Display | wwPDB validaton report |
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Full document | 7cdd_full_validation.pdf.gz | 772.2 KB | Display | |
Data in XML | 7cdd_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 7cdd_validation.cif.gz | 40.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/7cdd ftp://data.pdbj.org/pub/pdb/validation_reports/cd/7cdd | HTTPS FTP |
-Related structure data
Related structure data | 7cdcC 7cdeC 7cdfC 7cdgC 5h6qS 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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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 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: 15850.929 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 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1033.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 3 types, 90 molecules
#4: Chemical | ChemComp-FAD / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M N-(carbamoylmethyl)iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→48.97 Å / Num. obs: 66319 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.76→2.82 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4405 / CC1/2: 0.766 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H6Q Resolution: 2.76→45 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 10.815 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 84.366 Å2
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Refinement step | Cycle: 1 / Resolution: 2.76→45 Å
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