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Crystal structure of YTHDF2 in complex with M1A

Analyse Crystal structure of YTHDF2 in complex with M1A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7A1V
Type: protein
Length: 298 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yth domain-containing family protein 2
UniProt: Q9Y5A9
Ligands: M1A, SO4
Pockets: 4 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 29% 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	149	31% helix, 28% strand	Q9Y5A9

Ligands and binding sites

M1A · 6-amino-1-methylpurine · ligand · chains A
SO4 · Sulfate ion · ion · 7 copies · chains A, B
GOL · Glycerol · additive · chains B

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

Pockets

4 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	119	0.53	0.82	25	M1A
2	55	0.47	0.85	14	empty
3	64	0.38	0.79	18	empty
4	76	0.30	0.74	20	empty

Interfaces

1 interface between chains.

A–B · 459 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

7A1V · Crystal structure of YTHDF2 in complex with m1A · 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 0.96

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 7A1V · PDBe 7A1V · UniProt Q9Y5A9

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