SMTL ID : 7po6.3 (2 other biounits)

Xist (m6A)UCG tetraloop RNA bound to the YTH domain of YTHDC1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.135 Chain B: U.7, C.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.135 Salt bridges: A:R.135 SO4.3: 2 residues within 4Å: Chain A: R.111, E.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.112 Salt bridges: A:R.111 SO4.4: 4 residues within 4Å: Chain A: N.23, R.64, P.91, A.92 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.23, A:N.23, A:A.92 Salt bridges: A:R.64

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

EDO.2: 7 residues within 4Å: Chain A: H.25, V.28, S.29, K.32, V.63, Q.70, E.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.25, A:K.32

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 8 residues within 4Å: Chain A: T.39, L.40, P.41, E.44, M.98, L.99, G.100, G.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.98, A:G.101 Water bridges: A:T.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, A.N. et al., Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1. Nucleic Acids Res. (2022)

Release Date

2022-03-16

Peptides

Isoform 2 of YTH domain-containing protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Isoform 2 of YTH domain-containing protein 1

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