+Open data
-Basic information
Entry | Database: PDB / ID: 5fpl | ||||||
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Title | Crystal structure of human JARID1B in complex with CCT363901 | ||||||
Components | LYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE 5B | ||||||
Keywords | OXIDOREDUCTASE / LYSINE-SPECIFIC DEMETHYLASE 5B | ||||||
Function / homology | Function and homology information regulation of estradiol secretion / mammary duct terminal end bud growth / uterus morphogenesis / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of mammary gland epithelial cell proliferation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / lens fiber cell differentiation / histone H3K4 demethylase activity / cellular response to fibroblast growth factor stimulus ...regulation of estradiol secretion / mammary duct terminal end bud growth / uterus morphogenesis / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of mammary gland epithelial cell proliferation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / lens fiber cell differentiation / histone H3K4 demethylase activity / cellular response to fibroblast growth factor stimulus / branching involved in mammary gland duct morphogenesis / single fertilization / histone demethylase activity / response to fungicide / cellular response to leukemia inhibitory factor / post-embryonic development / Chromatin modifications during the maternal to zygotic transition (MZT) / HDMs demethylate histones / transcription corepressor activity / rhythmic process / sequence-specific double-stranded DNA binding / histone binding / nucleic acid binding / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Srikannathasan, V. / Yann-Vai, L.B. / Nowak, R. / Johansson, C. / Gileadi, C. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Brennan, P. ...Srikannathasan, V. / Yann-Vai, L.B. / Nowak, R. / Johansson, C. / Gileadi, C. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Brennan, P. / Huber, K. / Oppermann, U. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: 8-Substituted Pyrido[3,4-D]Pyrimidin-4(3H)-One Derivatives as Potent, Cell Permeable, Kdm4 (Jmjd2) and Kdm5 (Jarid1) Histone Lysine Demethylase Inhibitors. Authors: Bavetsias, V. / Lanigan, R.M. / Ruda, G.F. / Atrash, B. / Mclaughlin, M.G. / Tumber, A. / Mok, N.Y. / Le Bihan, Y. / Dempster, S. / Boxall, K.J. / Jeganathan, F. / Hatch, S.B. / Savitsky, P. ...Authors: Bavetsias, V. / Lanigan, R.M. / Ruda, G.F. / Atrash, B. / Mclaughlin, M.G. / Tumber, A. / Mok, N.Y. / Le Bihan, Y. / Dempster, S. / Boxall, K.J. / Jeganathan, F. / Hatch, S.B. / Savitsky, P. / Velupillai, S. / Krojer, T. / England, K.S. / Sejberg, J. / Thai, C. / Donovan, A. / Pal, A. / Scozzafava, G. / Bennett, J.M. / Kawamura, A. / Johansson, C. / Szykowska, A. / Gileadi, C. / Burgess-Brown, N.A. / von Delft, F. / Oppermann, U. / Walters, Z. / Shipley, J. / Raynaud, F.I. / Westaway, S.M. / Prinjha, R.K. / Fedorov, O. / Burke, R. / Schofield, C.J. / Westwood, I.M. / Bountra, C. / Muller, S. / Van Montfort, R.L.M. / Brennan, P.E. / Blagg, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fpl.cif.gz | 211.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fpl.ent.gz | 169.5 KB | Display | PDB format |
PDBx/mmJSON format | 5fpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/5fpl ftp://data.pdbj.org/pub/pdb/validation_reports/fp/5fpl | HTTPS FTP |
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-Related structure data
Related structure data | 5f2sC 5f2wC 5f32C 5f37C 5f39C 5f3cC 5f3eC 5f3gC 5f3iC 5f5aC 5f5cC 5f5iC 5a1fS 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 , 1 types, 1 molecules A
#1: Protein | Mass: 55370.570 Da / Num. of mol.: 1 / Fragment: JMJC DOMAIN, RESIDUES 25-101,374-772 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9UGL1 |
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-Non-polymers , 6 types, 286 molecules
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-QAY / | #5: Chemical | #6: Chemical | ChemComp-DMS / | #7: Water | ChemComp-HOH / | |
-Details
Sequence details | RESIDUE NUMBER 0-MET FROM THE CONSTRUCT. KDM5B START WITH PHE26. GGGG (101-105) FOUR GLYCINE LINKER ...RESIDUE NUMBER 0-MET FROM THE CONSTRUCT. KDM5B START WITH PHE26. GGGG (101-105) FOUR GLYCINE LINKER INTRODUCED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.05 Å3/Da / Density % sol: 69.65 % / Description: NONE |
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Crystal grow | pH: 8 Details: 0.1M HEPES PH 8.0, 0.8M POTASSIUM PHOSPHATE-DIBASIC, 0.8M SODIUM PHOSPHATE MONOBASIC |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2015 / Details: MIRRORS |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→46.17 Å / Num. obs: 38565 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 20.1 % / Biso Wilson estimate: 65.42 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 14.27 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 19.7 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 14.27 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5A1F Resolution: 2.35→46.17 Å / Cor.coef. Fo:Fc: 0.9433 / Cor.coef. Fo:Fc free: 0.9383 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.203 / SU Rfree Blow DPI: 0.162 / SU Rfree Cruickshank DPI: 0.158
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Displacement parameters | Biso mean: 65.2 Å2
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Refine analyze | Luzzati coordinate error obs: 0.286 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→46.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.41 Å / Total num. of bins used: 19
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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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