Research workbench
Yth domain of human YTHDC1 with dsdna comprising single N6MA joined by two six-bp DNA duplexes in P212121 crystal
Analyse Yth domain of human YTHDC1 with dsdna comprising single N6MA joined by two… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L4Y
- Type
- protein + DNA
- Length
- 190 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ssdna 13MER; Yth domain-containing protein 1
- UniProt
- Q96MU7
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, E | Ssdna 13MER | dna | 13 | — | — |
| B | Yth domain-containing protein 1 | protein | 164 | 34% helix, 24% strand | Q96MU7 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.34 | 0.79 | 11 | empty |
| 2 | 53 | 0.32 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–E · 779 Ų buried · 14 hydrogen bonds · protein-nucleic
- F–E · 297 Ų buried · 27 hydrogen bonds · nucleic-nucleic
- F–B · 189 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 7L4Y · YTH Domain of Human YTHDC1 with dsDNA Comprising Single N6mA joined by Two Six-bp DNA… · the same entry in another collection · chain F against F, 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
- Every structure of UniProt Q96MU7
- Elsewhere: RCSB PDB 7L4Y · PDBe 7L4Y · UniProt Q96MU7
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