SMTL ID : 6we8.2 (2 other biounits)

YTH domain of human YTHDC1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.18 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: A.116, H.117 No protein-ligand interaction detected (PLIP)

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

SO4.2: 3 residues within 4Å: Chain A: S.76, H.77, H.78 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.78 Water bridges: A:S.76, A:H.78 Salt bridges: A:H.77 SO4.4: 3 residues within 4Å: Chain A: G.1, S.3, K.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.1, A:S.3, A:K.4 Water bridges: A:T.2, A:T.2 Salt bridges: A:K.4

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: K.29, R.107, R.108, E.109 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.29, A:R.107 Water bridges: A:R.108, A:R.108, A:E.109 EDO.5: 3 residues within 4Å: Chain A: F.48, A.51, R.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.51 EDO.6: 5 residues within 4Å: Chain A: S.19, N.24, W.34, S.35, W.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.24 Water bridges: A:N.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Woodcock, C.B. et al., Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA. Nucleic Acids Res. (2020)

Release Date

2020-07-15

Peptides

YTH domain-containing protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

YTH domain-containing protein 1

Related Entries With Identical Sequence