Research workbench
Yth domain of human YTHDC1 with 11MER ssdna containing N6MA
Analyse Yth domain of human YTHDC1 with 11MER ssdna containing N6MA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WE9
- Type
- protein + DNA
- Length
- 347 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yth domain-containing protein 1; DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*CP*TP*G)-3')
- UniProt
- Q96MU7
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Yth domain-containing protein 1 | protein | 164 | 29% helix, 24% strand | Q96MU7 |
| B | DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*CP*TP*G)-3') | dna | 11 | — | — |
| F | DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*CP*TP*G)-3') | dna | 8 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.41 | 0.82 | 16 | empty |
| 2 | 76 | 0.40 | 0.78 | 17 | empty |
| 3 | 50 | 0.31 | 0.77 | 18 | empty |
| 4 | 50 | 0.26 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 795 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–F · 668 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–F · 223 Ų buried · 19 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6WE9 · YTH domain of human YTHDC1 with 11mer ssDNA Containing N6mA · the same entry in another collection · chain C against C, 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 6WE9 · PDBe 6WE9 · UniProt Q96MU7
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