Research workbench
The yth domain of YTHDC1 protein in complex with M6ACU oligonucleotide
Analyse The yth domain of YTHDC1 protein in complex with M6ACU oligonucleotide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RT4
- Type
- protein + RNA
- Length
- 326 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yth domain-containing protein 1; RNA (5'-R(*(6MZ)P*C)-3')
- UniProt
- Q96MU7
- Ligands
- 6MZ, SO4
- Pockets
- 6 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Yth domain-containing protein 1 | protein | 160 | 34% helix, 25% strand | Q96MU7 |
| A | Yth domain-containing protein 1 | protein | 163 | 32% helix, 26% strand | Q96MU7 |
| D | RNA (5'-R(*(6MZ)P*C)-3') | rna | 3 | — | — |
Ligands and binding sites
- 6MZ · N6-methyladenosine-5'-monophosphate · ligand · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.51 | 0.84 | 15 | 6MZ |
| 2 | 78 | 0.44 | 0.80 | 17 | empty |
| 3 | 114 | 0.44 | 0.77 | 15 | empty |
| 4 | 92 | 0.41 | 0.77 | 16 | empty |
| 5 | 115 | 0.35 | 0.73 | 19 | empty |
Interfaces
2 interfaces between chains.
- B–D · 588 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–A · 248 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6RT4 · The YTH domain of YTHDC1 protein in complex with m6ACU oligonucleotide · the same entry in another collection · chain D against D, TM-score 1.00
- Q96MU7 · AlphaFold monomer V2.0 prediction for yth domain-containing protein 1 (Q96MU7) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q96MU7
- Elsewhere: RCSB PDB 6RT4 · PDBe 6RT4 · UniProt Q96MU7
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