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Open data
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Basic information
Entry | Database: PDB / ID: 6zd5 | |||||||||
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Title | Crystal structure of YTHDC1 S378A mutant complex with m6A | |||||||||
![]() | YTH domain containing 1 | |||||||||
![]() | RNA BINDING PROTEIN / YTHDC1 / m6A / complex / inhibitor | |||||||||
Function / homology | N-methyladenosine![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bedi, R.K. / Li, Y. / Caflisch, A. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Atomistic and Thermodynamic Analysis of N6-Methyladenosine (m 6 A) Recognition by the Reader Domain of YTHDC1. Authors: Li, Y. / Bedi, R.K. / Wiedmer, L. / Sun, X. / Huang, D. / 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 | ![]() | 100.9 KB | Display | ![]() |
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PDB format | ![]() | 61.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ynnC ![]() 6ynoC ![]() 6zcmC ![]() 6zcnC ![]() 6zd3C ![]() 6zd4C ![]() 6zd7C ![]() 6zd8C ![]() 6zd9C ![]() 6zdaC ![]() 4r3hS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20951.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #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: 2.01 Å3/Da / Density % sol: 38.78 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 25% PEG3350, 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: Jun 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40.89 Å / Num. obs: 14545 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 22.21 Å2 / CC1/2: 0.998 / Net I/σ(I): 25.77 |
Reflection shell | Resolution: 2.3→2.44 Å / Num. unique obs: 2296 / CC1/2: 0.993 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4r3h Resolution: 2.3→40.89 Å / SU ML: 0.2654 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.1658 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: 22.87 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→40.89 Å
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Refine LS restraints |
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LS refinement shell |
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