SMTL ID : 7bik.2 (1 other biounit)

Crystal structure of YTHDF2 in complex with m6Am

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: Y.61, K.89, S.90, A.91 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.61, A:Y.61, A:A.91

1 x TV8: (2~{R},3~{S},4~{R},5~{R})-2-(hydroxymethyl)-4-methoxy-5-[6-(methylamino)purin-9-yl]oxolan-3-ol(Non-covalent)

TV8.2: 14 residues within 4Å: Chain A: K.31, S.32, Y.33, S.34, D.37, W.47, C.48, T.50, N.77, W.101, K.105, W.106, R.142, D.143 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.33, A:C.48, A:K.105, A:K.105, A:R.142 Water bridges: A:N.77, A:S.102, A:D.143 pi-Stacking: A:W.106, A:W.106, A:W.106

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 10 residues within 4Å: Chain A: K.31, S.75, V.76, N.77, G.78, S.79, G.80, H.81, N.122, T.139 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.75, A:V.76, A:G.78, A:S.79, A:G.80, A:H.81, A:N.122 Water bridges: A:K.31, A:K.31, A:K.31, A:K.31, A:T.139 Salt bridges: A:K.31 SO4.4: 1 residues within 4Å: Chain A: K.151 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.151 Salt bridges: A:K.151 SO4.5: 3 residues within 4Å: Chain A: N.122, R.126, T.139 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.122, A:T.139 Water bridges: A:T.139, A:N.140 Salt bridges: A:R.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X. et al., Crystal structure of YTHDF2 in complex with m6Am. To Be Published

Release Date

2021-11-24

Peptides

YTH domain-containing family protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

YTH domain-containing family protein 2

Related Entries With Identical Sequence