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- PDB-5nrs: Human DNMT3B PWWP domain in complex with N,N-bis(2-hydroxypropyl)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nrs | ||||||
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Title | Human DNMT3B PWWP domain in complex with N,N-bis(2-hydroxypropyl)ethanolamine | ||||||
![]() | DNA (cytosine-5)-methyltransferase 3B | ||||||
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Function / homology | ![]() : / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / DNA-methyltransferase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 68.9 KB | Display | ![]() |
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PDB format | ![]() | 50.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5nr3C ![]() 5nrrC ![]() 5nrvC ![]() 5nv0C ![]() 5nv2C ![]() 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, ![]() #2: Chemical | ChemComp-SO4 / ![]() #3: Chemical | #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.81 % |
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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 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→40.81 Å / Num. obs: 23390 / % possible obs: 99.5 % / Redundancy: 9.3 % / Biso Wilson estimate: 61.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.893 / Mean I/σ(I) obs: 1.89 / Num. unique all: 3609 / CC1/2: 0.614 / % possible all: 96.9 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3QKJ Resolution: 2.3→40.81 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.26
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.42 Å2 / Biso mean: 60.46 Å2 / Biso min: 32.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→40.81 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: 8
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