Research workbench
Xist (M6A)UCG tetraloop RNA bound to the yth domain of YTHDC1
Analyse Xist (M6A)UCG tetraloop RNA bound to the yth domain of YTHDC1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PO6
- Type
- protein + RNA
- Length
- 505 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*(6MZ)P*UP*C)-3'); Isoform 2 of yth domain-containing protein 1
- UniProt
- Q96MU7
- Ligands
- G, NA, SO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E | RNA (5'-R(*(6MZ)P*UP*C)-3') | rna | 3 | — | — |
| B | Isoform 2 of yth domain-containing protein 1 | protein | 166 | 36% helix, 24% strand | Q96MU7 |
| A | Isoform 2 of yth domain-containing protein 1 | protein | 163 | 34% helix, 26% strand | Q96MU7 |
| C | Isoform 2 of yth domain-containing protein 1 | protein | 166 | 36% helix, 24% strand | Q96MU7 |
| F | RNA (5'-R(*(6MZ)P*UP*C)-3') | rna | 4 | — | — |
Ligands and binding sites
- G · Guanosine-5'-monophosphate · ligand · chains D, B
- NA · Sodium ion · metal · chains C
- SO4 · Sulfate ion · ion · 7 copies · chains B, D, A, C, F
- EDO · 1,2-ethanediol · additive · 7 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.72 | 0.86 | 31 | EDO |
| 2 | 687 | 0.70 | 0.77 | 71 | SO4 |
| 3 | 141 | 0.44 | 0.76 | 19 | SO4, EDO |
| 4 | 107 | 0.42 | 0.77 | 23 | empty |
| 5 | 73 | 0.42 | 0.80 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–F · 635 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–A · 631 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 617 Ų buried · 17 hydrogen bonds · protein-nucleic
- D–B · 588 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–C · 307 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 7PO6 · Xist (m6A)UCG tetraloop RNA bound to the YTH domain of YTHDC1 · the same entry in another collection · chain F against F, TM-score 1.00
- Q96MU7 · AlphaFold monomer V2.0 prediction for yth domain-containing protein 1 (Q96MU7) · a predicted model of the same protein · chain A 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 Q96MU7
- Elsewhere: RCSB PDB 7PO6 · PDBe 7PO6 · UniProt Q96MU7
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