Research workbench
Crystal structure of YTHDC1 apo purified using GST tag
Analyse Crystal structure of YTHDC1 apo purified using GST tag in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZD9
- Type
- protein
- Length
- 328 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YTHDC1
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | YTHDC1 | protein | 164 | 33% helix, 25% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.70 | 0.87 | 32 | SO4 |
| 2 | 129 | 0.54 | 0.82 | 21 | empty |
| 3 | 66 | 0.48 | 0.84 | 16 | SO4 |
| 4 | 102 | 0.41 | 0.76 | 17 | empty |
| 5 | 54 | 0.28 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 577 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6ZD9 · Crystal structure of YTHDC1 apo purified using GST tag · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6ZD9 · PDBe 6ZD9
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