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- PDB-5nv2: Human DNMT3B PWWP domain in complex with N-isopropyl-1,5-dimethyl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nv2 | ||||||
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Title | Human DNMT3B PWWP domain in complex with N-isopropyl-1,5-dimethylhexylamine (Metron S) | ||||||
![]() | DNA (cytosine-5)-methyltransferase 3B | ||||||
![]() | TRANSFERASE / DNMT3B PWWP DOMAIN / HISTONE BINDING / BETA BARREL / LIGAND | ||||||
Function / homology | ![]() DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / catalytic complex / DNA methylation / PRC2 methylates histones and DNA / Defective pyroptosis / NoRC negatively regulates rRNA expression ...DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / catalytic complex / DNA methylation / PRC2 methylates histones and DNA / Defective pyroptosis / NoRC negatively regulates rRNA expression / transcription corepressor activity / methylation / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rondelet, G. / Wouters, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Targeting PWWP domain of DNA methyltransferase 3B for epigenetic cancer therapy: Identification and structural characterization of new potential protein-protein interaction inhibitors Authors: Rondelet, G. / Dal Maso, T. / Maniquet, A. / Themans, Q. / Wouters, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.3 KB | Display | ![]() |
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PDB format | ![]() | 52.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.7 KB | Display | ![]() |
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Full document | ![]() | 463.6 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nr3C ![]() 5nrrC ![]() 5nrsC ![]() 5nrvC ![]() 5nv0C ![]() 5nv7C ![]() 5nvoC ![]() 3qkjS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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
#1: Protein | Mass: 16698.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UBC3, DNA (cytosine-5-)-methyltransferase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350 / PH range: 5.7-6.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2015 |
Radiation | Monochromator: channel cut monochromator crystal (Si(111)) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.029→40.62 Å / Num. obs: 33473 / % possible obs: 99.9 % / Redundancy: 9.8 % / Biso Wilson estimate: 50.72 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.042 / Net I/σ(I): 26.76 |
Reflection shell | Resolution: 2.03→2.15 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.38 / Num. unique obs: 5331 / CC1/2: 0.54 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3QKJ Resolution: 2.029→40.62 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.68 Å2 / Biso mean: 50.7 Å2 / Biso min: 25.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.029→40.62 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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