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- PDB-8q4u: Crystal structure of YTHDC1 in complex with Compound 36 (ZA_540b) -
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Open data
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Basic information
Entry | Database: PDB / ID: 8q4u | ||||||
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Title | Crystal structure of YTHDC1 in complex with Compound 36 (ZA_540b) | ||||||
![]() | YTH domain-containing protein 1 | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / dosage compensation by inactivation of X chromosome / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bedi, R.K. / Zalesak, F. / Caflisch, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of YTHDC1 in complex with Compound 36 (ZA_540b) Authors: Bedi, R.K. / Zalesak, F. / Caflisch, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.5 KB | Display | ![]() |
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PDB format | ![]() | 63 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18823.826 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-SO4 / ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.05 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 25% PEG 3350, 0.2M Ammonium Sulphate, 0.1M Bis-Tris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 22, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.37→38.7 Å / Num. obs: 68786 / % possible obs: 98.4 % / Redundancy: 3.37 % / Biso Wilson estimate: 24.13 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.37→1.45 Å / Num. unique obs: 10882 / CC1/2: 0.647 |
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Processing
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Refinement | Method to determine structure![]() ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→38.7 Å
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Refine LS restraints |
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LS refinement shell |
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