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Yorodumi- PDB-7cd9: Crystal Structure of SETDB1 tudor domain in complexed with Compound 6 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cd9 | ||||||
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Title | Crystal Structure of SETDB1 tudor domain in complexed with Compound 6 | ||||||
Components | Histone-lysine N-methyltransferase SETDB1 | ||||||
Keywords | TRANSFERASE / SETDB1 / Tudor domain / inhibitor | ||||||
Function / homology | Function and homology information [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / positive regulation of DNA methylation-dependent heterochromatin formation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / heterochromatin organization / promoter-specific chromatin binding / PKMTs methylate histone lysines ...[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / positive regulation of DNA methylation-dependent heterochromatin formation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / heterochromatin organization / promoter-specific chromatin binding / PKMTs methylate histone lysines / chromosome / methylation / negative regulation of gene expression / intracellular membrane-bounded organelle / chromatin binding / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Xiong, L. / Guo, Y. / Mao, X. / Huang, L. / Wu, C. / Yang, S. | ||||||
Funding support | China, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: Structure-Guided Discovery of a Potent and Selective Cell-Active Inhibitor of SETDB1 Tudor Domain. Authors: Guo, Y. / Mao, X. / Xiong, L. / Xia, A. / You, J. / Lin, G. / Wu, C. / Huang, L. / Wang, Y. / Yang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cd9.cif.gz | 190.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cd9.ent.gz | 151.5 KB | Display | PDB format |
PDBx/mmJSON format | 7cd9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cd9_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7cd9_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7cd9_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 7cd9_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/7cd9 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/7cd9 | HTTPS FTP |
-Related structure data
Related structure data | 7c9nC 7cajC 7cjtC 6bhdS 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
#1: Protein | Mass: 27613.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SETDB1, ESET, KIAA0067, KMT1E / Production host: Escherichia coli (E. coli) References: UniProt: Q15047, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | 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: 46.19 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.2 M Sodium citrate tribasic dihydrate 20% PEG3350 PH 8.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97849 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97849 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 64717 / % possible obs: 98.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 12.52 Å2 / CC1/2: 0.996 / Net I/σ(I): 30.257 |
Reflection shell | Resolution: 1.6→1.63 Å / Num. unique obs: 3196 / CC1/2: 0.996 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BHD Resolution: 1.6→29.662 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.67 / 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: 102.98 Å2 / Biso mean: 21.0988 Å2 / Biso min: 2.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→29.662 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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