SMTL ID : 6sz1.2 (1 other biounit)

Crystal structure of YTHDC1 with fragment 2 (DHU_DC1_140)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x M0W: ~{N}-methylquinazolin-4-amine(Non-covalent)

M0W.1: 12 residues within 4Å: Chain A: K.35, S.36, N.37, N.41, W.51, S.52, T.53, W.102, P.105, M.108, L.113, D.150 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.51, A:L.113 Hydrogen bonds: A:N.37, A:N.41, A:S.52

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

SO4.2: 2 residues within 4Å: Chain A: R.125, E.126 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.126 Water bridges: A:R.125, A:R.125 Salt bridges: A:R.125 SO4.3: 2 residues within 4Å: Chain A: K.60, E.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.153 Water bridges: A:K.60 Salt bridges: A:K.60 SO4.4: 1 residues within 4Å: Chain A: R.125 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.125 SO4.5: 3 residues within 4Å: Chain A: K.59, N.62, R.66 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.62 Salt bridges: A:K.59, A:R.66

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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