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Yorodumi- PDB-7t7l: Structure of human G9a SET-domain (EHMT2) in complex with covalen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7t7l | ||||||
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Title | Structure of human G9a SET-domain (EHMT2) in complex with covalent inhibitor (Compound 1) | ||||||
Components | Histone-lysine N-methyltransferase EHMT2 | ||||||
Keywords | GENE REGULATION / G9a / Covalent inhibitor | ||||||
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: 2.2 Å | ||||||
Authors | Park, K.-S. / Kumar, P. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Discovery of the First-in-Class G9a/GLP Covalent Inhibitors. Authors: Park, K.S. / Xiong, Y. / Yim, H. / Velez, J. / Babault, N. / Kumar, P. / Liu, J. / Jin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t7l.cif.gz | 242.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t7l.ent.gz | 191.7 KB | Display | PDB format |
PDBx/mmJSON format | 7t7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t7l_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 7t7l_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 7t7l_validation.xml.gz | 47.1 KB | Display | |
Data in CIF | 7t7l_validation.cif.gz | 61.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/7t7l ftp://data.pdbj.org/pub/pdb/validation_reports/t7/7t7l | HTTPS FTP |
-Related structure data
Related structure data | 7t7mC 5ttfS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 32604.924 Da / Num. of mol.: 4 / Fragment: residues 913-1193 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT2, BAT8, C6orf30, G9A, KMT1C, NG36 / Production host: Escherichia coli (E. coli) References: UniProt: Q96KQ7, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase |
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-Non-polymers , 5 types, 369 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SAM / #4: Chemical | #5: Chemical | ChemComp-G4R / | #6: 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: 2.54 Å3/Da / Density % sol: 51.5 % |
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Crystal grow | Temperature: 290.15 K / Method: vapor diffusion, sitting drop Details: 2% v/v 1,4-Dioxane, 10% w/v Polyethylene glycol 20,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.959→80.299 Å / Num. all: 63720 / Num. obs: 63720 / % possible obs: 98.2 % / Redundancy: 2.4 % / Biso Wilson estimate: 31 Å2 / Rpim(I) all: 0.058 / Rrim(I) all: 0.089 / Rsym value: 0.067 / Net I/av σ(I): 8.3 / Net I/σ(I): 8.9 / Num. measured all: 152076 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TTF Resolution: 2.2→68.425 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 30.95 / Stereochemistry target values: ML
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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 max: 95.72 Å2 / Biso mean: 44.2625 Å2 / Biso min: 21.76 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→68.425 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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