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Crystal structure of N6-methyladenosine RNA reader YTHDF2

Analyse Crystal structure of N6-methyladenosine RNA reader YTHDF2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WQN
Type: protein
Length: 302 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yth domain-containing family protein 2
UniProt: Q9Y5A9
Pockets: 3 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Yth domain-containing family protein 2	protein	151	28% helix, 28% strand	Q9Y5A9

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 2 copies · chains B
GOL · Glycerol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	176	0.48	0.76	39	empty
2	56	0.35	0.78	19	empty
3	66	0.30	0.75	18	empty

Interfaces

1 interface between chains.

A–B · 332 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4WQN · Crystal structure of N6-methyladenosine RNA reader YTHDF2 · 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 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 Q9Y5A9
Elsewhere: RCSB PDB 4WQN · PDBe 4WQN · UniProt Q9Y5A9

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