Research workbench
Yth domain of human YTHDC1 with dsdna comprising single N6MA joined by two six-bp DNA duplexes in P3221 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
- 7L4X
- Type
- protein + DNA
- Length
- 178 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yth domain-containing protein 1; Ssdna W/N6A
- UniProt
- Q96MU7
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Yth domain-containing protein 1 | protein | 165 | 32% helix, 25% strand | Q96MU7 |
| E | Ssdna W/N6A | dna | 13 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, E
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 | 85 | 0.37 | 0.76 | 15 | empty |
| 2 | 91 | 0.35 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- B–E · 739 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7L4X · YTH Domain of Human YTHDC1 with dsDNA Comprising Single N6mA joined by two six-bp DNA… · the same entry in another collection · chain B against B, 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 7L4X · PDBe 7L4X · UniProt Q96MU7
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