Research workbench

Structure of YTH-YTHDF2 in complex with m6A

Analyse Structure of YTH-YTHDF2 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: 4RDN
Type: protein
Length: 297 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.1
Source: Homo sapiens
Molecule: YTH domain-containing family protein 2
UniProt: Q9Y5A9
Ligands: 6MD, SO4
Pockets: 2 · best druggability 0.54

Structure

x-ray diffraction · resolution 2.1 · 2 distinct chains · 29% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YTH domain-containing family protein 2	protein	149	29% helix, 30% strand	Q9Y5A9
B	YTH domain-containing family protein 2	protein	148	29% helix, 30% strand	Q9Y5A9

Ligands and binding sites

6MD · N-methyladenosine · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	147	0.54	0.81	31	6MD
2	143	0.47	0.77	35	6MD, SO4

Interfaces

1 interface between chains.

A–B · 437 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

4RDN · Structure of yth-YTHDF2 in complex with M6A · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y5A9 · AlphaFold monomer V2.0 prediction for yth domain-containing family protein 2 (Q9Y5A9) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 Q9Y5A9
Elsewhere: RCSB PDB 4RDN · PDBe 4RDN · UniProt Q9Y5A9

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.