SMTL ID : 9h2y.1 (1 other biounit)

Crystal structure of YTHDC1 in complex with AI_056

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

monomer

Ligands

2 x 01: 3-sulfanyl-1,2,4-triazin-5-ol

01.1: 9 residues within 4Å: Chain A: S.19, N.20, N.24, W.34, S.35, T.36, W.85, L.96, D.133 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.20, A:N.24, A:S.35 pi-Stacking: A:W.34 01.2: 5 residues within 4Å: Chain A: V.33, S.81, I.83, V.99, K.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.81, A:S.81

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

SO4.3: 4 residues within 4Å: Chain A: G.1, T.2, 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:S.3, A:L.5 Salt bridges: A:K.4 SO4.4: 1 residues within 4Å: Chain A: P.82 No protein-ligand interaction detected (PLIP) SO4.5: 2 residues within 4Å: Chain A: 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

Bedi, R.K. et al., Crystal structure of YTHDC1 in complex with AI_056. To Be Published

Release Date

2025-08-27

Peptides

YTH domain-containing protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

YTH domain-containing protein 1

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