SMTL ID : 7po6.1 (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

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 5 residues within 4Å: Chain A: C.8 Chain B: E.65, G.67, F.115, K.132 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.132

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

EDO.2: 6 residues within 4Å: Chain B: H.25, V.28, S.29, K.32, V.63, Q.70 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.25, B:K.32 Water bridges: B:S.29, B:Q.70 EDO.4: 5 residues within 4Å: Chain B: H.25, V.63, R.64, E.65, S.66 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain B: R.110, R.111, D.155, S.157, I.158 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.110, B:R.110, B:R.111, B:S.157 EDO.8: 10 residues within 4Å: Chain B: L.8, F.72, I.108, C.109, F.152, P.153, P.154, D.155, I.158, L.160 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.108, B:F.152, B:D.155

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

SO4.3: 3 residues within 4Å: Chain B: N.23, P.91, A.92 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.23, B:A.92 SO4.5: 4 residues within 4Å: Chain A: U.7, C.8 Chain B: R.64, R.135 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.64 Salt bridges: B:R.135 SO4.7: 2 residues within 4Å: Chain B: R.111, P.153 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.112 Salt bridges: B:R.111

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: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
B

Isoform 2 of YTH domain-containing protein 1

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