Research workbench
Crystal structure of the PHO92 yth domain in complex with M6A
Analyse Crystal structure of the PHO92 yth domain in complex with M6A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RCM
- Type
- protein
- Length
- 323 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylated RNA-binding protein 1
- UniProt
- Q06390
- Ligands
- 6MZ, UNX
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylated RNA-binding protein 1 | protein | 164 | 28% helix, 27% strand | Q06390 |
| B | Methylated RNA-binding protein 1 | protein | 159 | 31% helix, 28% strand | Q06390 |
Ligands and binding sites
- 6MZ · N6-methyladenosine-5'-monophosphate · ligand · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 19 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.80 | 0.85 | 57 | UNX |
| 2 | 150 | 0.48 | 0.77 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 682 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4RCM · Crystal structure of the Pho92 YTH domain in complex with m6A · the same entry in another collection · chain B against B, TM-score 1.00
- Q06390 · AlphaFold monomer V2.0 prediction for methylated RNA-binding protein 1 (Q06390) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q06390
- Elsewhere: RCSB PDB 4RCM · PDBe 4RCM · UniProt Q06390
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