+Open data
-Basic information
Entry | Database: PDB / ID: 7xub | ||||||
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Title | Structure of G9a in complex with compound 10d | ||||||
Components | Histone-lysine N-methyltransferase EHMT2 | ||||||
Keywords | TRANSFERASE / histone lysine methyltransferase / inhibitor / protein-inhibitor complex | ||||||
Function / homology | Function and homology information 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 / DNA methylation-dependent heterochromatin formation / oocyte development / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / fertilization / 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 / enzyme binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Niwa, H. / Shirai, F. / Sato, S. / Nishigaya, Y. / Umehara, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: J.Med.Chem. / Year: 2023 Title: Discovery of Novel Substrate-Competitive Lysine Methyltransferase G9a Inhibitors as Anticancer Agents. Authors: Nishigaya, Y. / Takase, S. / Sumiya, T. / Kikuzato, K. / Sato, T. / Niwa, H. / Sato, S. / Nakata, A. / Sonoda, T. / Hashimoto, N. / Namie, R. / Honma, T. / Umehara, T. / Shirouzu, M. / ...Authors: Nishigaya, Y. / Takase, S. / Sumiya, T. / Kikuzato, K. / Sato, T. / Niwa, H. / Sato, S. / Nakata, A. / Sonoda, T. / Hashimoto, N. / Namie, R. / Honma, T. / Umehara, T. / Shirouzu, M. / Koyama, H. / Yoshida, M. / Ito, A. / Shirai, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xub.cif.gz | 293.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xub.ent.gz | 196.2 KB | Display | PDB format |
PDBx/mmJSON format | 7xub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xub_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7xub_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7xub_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 7xub_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/7xub ftp://data.pdbj.org/pub/pdb/validation_reports/xu/7xub | HTTPS FTP |
-Related structure data
Related structure data | 7xuaSC 7xucC 7xudC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 32604.924 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free synthesis / Gene: EHMT2, BAT8, C6orf30, G9A, KMT1C, NG36 / Production host: Escherichia coli (E. coli) References: UniProt: Q96KQ7, Transferases; Transferring one-carbon groups; Methyltransferases |
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-Non-polymers , 6 types, 314 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-TRS / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.29 Å3/Da / Density % sol: 46.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M Bis-Tris propane (7.75), 0.2M Sodium Formate, 10% Ethylene Glycol, 26% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Oct 19, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 40123 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 30.49 Å2 / Rsym value: 0.1 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2→2.03 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2004 / Rsym value: 0.93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7XUA Resolution: 2→38.05 Å / SU ML: 0.253 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 26.6286 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→38.05 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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