+Open data
-Basic information
Entry | Database: PDB / ID: 7msb | ||||||
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Title | Structure of EED bound to EEDi-4259 | ||||||
Components | Polycomb protein EED | ||||||
Keywords | GENE REGULATION/INHIBITOR / polycomb repressive complex 2 / GENE REGULATION-INHIBITOR complex | ||||||
Function / homology | Function and homology information ESC/E(Z) complex / spinal cord development / histone methyltransferase activity / Transcriptional Regulation by E2F6 / enzyme activator activity / transcription corepressor binding / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / PKMTs methylate histone lysines ...ESC/E(Z) complex / spinal cord development / histone methyltransferase activity / Transcriptional Regulation by E2F6 / enzyme activator activity / transcription corepressor binding / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / chromosome / Oxidative Stress Induced Senescence / negative regulation of DNA-templated transcription / chromatin binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Petrunak, E. / Stuckey, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2021 Title: Discovery of EEDi-5273 as an Exceptionally Potent and Orally Efficacious EED Inhibitor Capable of Achieving Complete and Persistent Tumor Regression. Authors: Rej, R.K. / Wang, C. / Lu, J. / Wang, M. / Petrunak, E. / Zawacki, K.P. / McEachern, D. / Yang, C.Y. / Wang, L. / Li, R. / Chinnaswamy, K. / Wen, B. / Sun, D. / Stuckey, J.A. / Zhou, Y. / ...Authors: Rej, R.K. / Wang, C. / Lu, J. / Wang, M. / Petrunak, E. / Zawacki, K.P. / McEachern, D. / Yang, C.Y. / Wang, L. / Li, R. / Chinnaswamy, K. / Wen, B. / Sun, D. / Stuckey, J.A. / Zhou, Y. / Chen, J. / Tang, G. / Wang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7msb.cif.gz | 100.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7msb.ent.gz | 72.2 KB | Display | PDB format |
PDBx/mmJSON format | 7msb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/7msb ftp://data.pdbj.org/pub/pdb/validation_reports/ms/7msb | HTTPS FTP |
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-Related 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: 42412.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Escherichia coli (E. coli) / References: UniProt: O75530 |
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#2: Chemical | ChemComp-ZNG / ( |
#3: Water | ChemComp-HOH / |
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: 2.67 Å3/Da / Density % sol: 53.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2uL of protein + 2 uL of well (0.1 M Tris pH 8.5, 20% glycerol, 4.3 M Na Formate, 10 mM TCEP) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 4, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 36678 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 21.61 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.037 / Rrim(I) all: 0.101 / Χ2: 0.947 / Net I/σ(I): 7.3 / Num. measured all: 269118 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: in house structure Resolution: 1.9→18 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.128 / SU Rfree Blow DPI: 0.115 / SU Rfree Cruickshank DPI: 0.109
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Displacement parameters | Biso max: 108.43 Å2 / Biso mean: 23.28 Å2 / Biso min: 8.71 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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