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- PDB-7sff: Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7sff | ||||||
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Title | Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3852279B | ||||||
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![]() | TRANSFERASE/TRANSFERASE INHIBITOR / epigentics / DNA methytransferase fold / maintenance methylation / ![]() ![]() | ||||||
Function / homology | ![]() chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / epigenetic programming of gene expression / cellular response to bisphenol A / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA-methyltransferase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Horton, J.R. / Pathuri, S. / Cheng, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors. Authors: Horton, J.R. / Pathuri, S. / Wong, K. / Ren, R. / Rueda, L. / Fosbenner, D.T. / Heerding, D.A. / McCabe, M.T. / Pappalardi, M.B. / Zhang, X. / King, B.W. / Cheng, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 460.7 KB | Display | ![]() |
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PDB format | ![]() | 305.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7sfcC ![]() 7sfdC ![]() 7sfeC ![]() 7sfgC ![]() 6x9jS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 98803.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P26358, ![]() |
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-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 3678.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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#3: DNA chain | Mass: 3665.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Non-polymers , 5 types, 361 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/C79.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/GOL.gif)
![](data/chem/img/C79.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-EDO / ![]() #6: Chemical | ChemComp-GOL / | ![]() #7: Chemical | ChemComp-C79 / ( | #8: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.46 % |
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Crystal grow![]() | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.1 Details: 14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1) |
-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: Apr 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.05→38.75 Å / Num. obs: 71672 / % possible obs: 97.2 % / Redundancy: 5 % / Biso Wilson estimate: 36.65 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.039 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6373 / CC1/2: 0.591 / Rpim(I) all: 0.395 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6X9J Resolution: 2.05→38.75 Å / SU ML: 0.2547 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.3733 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: 54.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→38.75 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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