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- PDB-7buc: Crystal structure of EHMT2 SET domain in complex with compound 13 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7buc | ||||||
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Title | Crystal structure of EHMT2 SET domain in complex with compound 13 | ||||||
![]() | Histone-lysine N-methyltransferase EHMT2 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / PROTEIN-SMALL MOLECULE INHIBITOR COMPLEX / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() regulation of protein modification process / histone H3K56 methyltransferase activity / phenotypic switching / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / synaptonemal complex assembly ...regulation of protein modification process / histone H3K56 methyltransferase activity / phenotypic switching / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / synaptonemal complex assembly / negative regulation of autophagosome assembly / oocyte development / protein-lysine N-methyltransferase activity / fertilization / C2H2 zinc finger domain binding / DNA methylation-dependent heterochromatin formation / cellular response to cocaine / negative regulation of gene expression via chromosomal CpG island methylation / organ growth / Transcriptional Regulation by E2F6 / regulation of DNA replication / RNA Polymerase I Transcription Initiation / behavioral response to cocaine / Transcriptional Regulation by VENTX / spermatid development / long-term memory / response to fungicide / cellular response to starvation / Transferases; Transferring one-carbon groups; Methyltransferases / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / cellular response to xenobiotic stimulus / Senescence-Associated Secretory Phenotype (SASP) / response to ethanol / nuclear speck / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Suzuki, M. / Mizuno, M. / Katayama, K. | ||||||
![]() | ![]() Title: Discovery of novel histone lysine methyltransferase G9a/GLP (EHMT2/1) inhibitors: Design, synthesis, and structure-activity relationships of 2,4-diamino-6-methylpyrimidines. Authors: Katayama, K. / Ishii, K. / Tsuda, E. / Yotsumoto, K. / Hiramoto, K. / Suzuki, M. / Yasumatsu, I. / Igarashi, W. / Torihata, M. / Ishiyama, T. / Katagiri, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.3 KB | Display | ![]() |
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PDB format | ![]() | 94.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7btvC ![]() 5vseS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32604.924 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96KQ7, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M magnesium acetate, 20% polyethyleneglycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→78.43 Å / Num. obs: 19580 / % possible obs: 99.3 % / Redundancy: 3.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.078 / Rrim(I) all: 0.141 / Net I/σ(I): 6.8 / Num. measured all: 60135 / Scaling rejects: 21 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5VSE Resolution: 2.6→25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.903 / SU B: 17.319 / SU ML: 0.327 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.042 / ESU R Free: 0.335 / Details: 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 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.49 Å2 / Biso mean: 48.87 Å2 / Biso min: 24.32 Å2
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Refinement step | Cycle: final / Resolution: 2.6→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.69 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
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