SMTL ID : 8k2e.2 (1 other biounit)

Crystal structure of YTHDC1 and Y3 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x VIM: 2-chloranyl-6-(4-fluoranylphenoxy)benzoic acid(Non-covalent)

VIM.1: 16 residues within 4Å: Chain A: S.20, N.21, N.22, N.25, V.26, W.35, S.36, L.38, W.86, V.87, L.88, P.89, M.92, S.93, M.96, L.97 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.25, A:W.86, A:W.86, A:L.88, A:L.97 Hydrogen bonds: A:N.21, A:N.21, A:N.22, A:N.25 Halogen bonds: A:S.93

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

SO4.2: 4 residues within 4Å: Chain A: K.44, W.123, Q.136, E.137 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.135, A:Q.136, A:E.137 Water bridges: A:K.44, A:K.44 Salt bridges: A:K.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, Y. et al., PocketFlow is a data-and-knowledge-driven structure-based molecular generative model. Nat. Mach. Intell. (2024)

Release Date

2024-07-17

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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