SMTL ID : 6rt7.1 (1 other biounit)

The YTH domain of YTHDC1 protein in complex with Gm6ACU oligonucleotide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

1 x 6MZ- C: RNA (5'-R(*(6MZ)P*C)-3')(Non-covalent)

6MZ-C.1: 11 residues within 4Å: Chain A: K.18, S.19, N.20, N.24, W.34, S.35, W.85, M.91, L.96, R.132, D.133 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.18, A:N.20, A:N.20, A:N.24, A:S.35

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

SO4.2: 2 residues within 4Å: Chain A: R.108, E.109 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.109 Salt bridges: A:R.108 SO4.3: 2 residues within 4Å: Chain A: G.1, K.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.1 Salt bridges: A:K.4 SO4.4: 3 residues within 4Å: Chain A: S.76, H.77, H.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Flexible Binding of m6A Reader Protein YTHDC1 to Its Preferred RNA Motif. J Chem Theory Comput (2019)

Release Date

2019-11-27

Peptides

YTH domain-containing protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

YTH domain-containing protein 1

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