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- PDB-7sfe: 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: 7sfe | ||||||
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Title | Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830334A | ||||||
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![]() | TRANSFERASE/TRANSFERASE INHIBITOR / epigentics / DNA methytransferase fold / maintenance methylation / inhibition / DNA binding protein / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / STAT3 nuclear events downstream of ALK signaling ...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 / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / STAT3 nuclear events downstream of ALK signaling / female germ cell nucleus / methyl-CpG binding / DNA methylation-dependent heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / pericentric heterochromatin / Nuclear events stimulated by ALK signaling in cancer / positive regulation of vascular associated smooth muscle cell proliferation / DNA methylation / PRC2 methylates histones and DNA / replication fork / Defective pyroptosis / promoter-specific chromatin binding / cellular response to amino acid stimulus / NoRC negatively regulates rRNA expression / methylation / negative regulation of gene expression / DNA-templated transcription / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus 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 | ![]() | 459.1 KB | Display | ![]() |
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PDB format | ![]() | 305.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7sfcC ![]() 7sfdC ![]() 7sffC ![]() 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
-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, DNA (cytosine-5-)-methyltransferase |
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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, 236 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/96I.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/96I.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Chemical | ChemComp-96I / ( | #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: 2.85 Å3/Da / Density % sol: 56.9 % |
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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: Jun 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→42.14 Å / Num. obs: 38168 / % possible obs: 98 % / Redundancy: 5.5 % / Biso Wilson estimate: 54.1 Å2 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.064 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.55→2.64 Å / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3527 / CC1/2: 0.429 / Rpim(I) all: 0.492 / % possible all: 91.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6X9J Resolution: 2.55→42.13 Å / SU ML: 0.3692 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0724 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: 71.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→42.13 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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