MolNFT v1 · #168371 · protein + DNA
Yth domain of human YTHDC1 with a 10MER oligo containing N6MA
6WEA · Yth domain-containing protein 1: “Yth domain of human YTHDC1 with a 10MER oligo containing N6MA”. X-ray diffraction, 2 ligands (NA, SO4), 6 pockets (best druggability 0.73). MolNFT v1 #168371 on GenesisL1: 3D structure, binding…
- PDB
- 6WEA
- Type
- protein + DNA
- Length
- 691 residues
- Chains
- 8
- 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*TP*C)-3')
- UniProt
- Q96MU7
- Ligands
- NA, SO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Yth domain-containing protein 1 | protein | 163 | 34% helix, 26% strand | Q96MU7 |
| D | Yth domain-containing protein 1 | protein | 162 | 33% helix, 26% strand | Q96MU7 |
| E, F, G, H | DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*TP*C)-3') | dna | 10 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 13 copies · chains A, E, B, G, C, D
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, E, B, C, D, G
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 | 319 | 0.73 | 0.86 | 31 | EDO, NA |
| 2 | 98 | 0.40 | 0.76 | 12 | empty |
| 3 | 69 | 0.35 | 0.76 | 13 | empty |
| 4 | 110 | 0.35 | 0.73 | 19 | empty |
| 5 | 53 | 0.33 | 0.77 | 13 | empty |
Interfaces
7 interfaces between chains.
- D–H · 815 Ų buried · 17 hydrogen bonds · protein-nucleic
- C–F · 800 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–G · 771 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–E · 764 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–B · 566 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6WEA · YTH domain of human YTHDC1 with a 10mer Oligo Containing N6mA · the same entry in another collection · chain A against A, 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 6WEA · PDBe 6WEA · UniProt Q96MU7
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