SMTL ID : 6sz2.2 (1 other biounit)

Crystal structure of YTHDC1 with fragment 3 (DHU_DC1_149)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

monomer

Ligands

1 x M0Q: ~{N}-methyl-1,6-naphthyridin-4-amine(Non-covalent)

M0Q.1: 10 residues within 4Å: Chain A: N.41, W.51, S.52, T.53, L.54, W.102, P.105, M.108, L.113, D.150 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.113 Hydrogen bonds: A:S.52, A:L.54 Water bridges: A:N.37

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

SO4.2: 2 residues within 4Å: Chain A: R.125, E.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.126 Water bridges: A:R.125 Salt bridges: A:R.125 SO4.3: 1 residues within 4Å: Chain A: R.125 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.125 Salt bridges: A:R.125 SO4.4: 3 residues within 4Å: Chain A: R.78, R.149, D.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.150 Salt bridges: A:R.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bedi, R.K. et al., Selectively Disrupting m6A-Dependent Protein-RNA Interactions with Fragments. Acs Chem.Biol. (2020)

Release Date

2020-03-04

Peptides

YTH domain-containing protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

YTH domain-containing protein 1

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