Research workbench
Crystal structure of YTHDF3 yth domain in complex with M6A RNA
Analyse Crystal structure of YTHDF3 yth domain in complex with M6A RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZOT
- Type
- protein + RNA
- Length
- 334 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yth domain-containing family protein 3; RNA
- UniProt
- Q7Z739
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Yth domain-containing family protein 3 | protein | 180 | 34% helix, 25% strand | Q7Z739 |
| A | Yth domain-containing family protein 3 | protein | 150 | 33% helix, 31% strand | Q7Z739 |
| C | RNA | rna | 4 | — | — |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.63 | 0.79 | 52 | empty |
| 2 | 50 | 0.30 | 0.77 | 9 | empty |
Interfaces
3 interfaces between chains.
- B–A · 783 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 607 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 117 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6ZOT · Crystal structure of YTHDF3 YTH domain in complex with m6A RNA · the same entry in another collection · chain B against B, TM-score 1.00
- Q7Z739 · AlphaFold monomer V2.0 prediction for yth domain-containing family protein 3 (Q7Z739) · a predicted model of the same protein · chain B 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 Q7Z739
- Elsewhere: RCSB PDB 6ZOT · PDBe 6ZOT · UniProt Q7Z739
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