SMTL ID : 6sz3.2 (1 other biounit)

Crystal structure of YTHDC1 with fragment 4 (DHU_DC1_158)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

monomer

Ligands

2 x M1H: ~{N}-methyl-5,6,7,8-tetrahydroquinolin-4-amine(Non-covalent)

M1H.1: 1 residues within 4Å: Chain A: Y.24 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.24 Water bridges: A:R.69 pi-Stacking: A:Y.24 M1H.2: 7 residues within 4Å: Chain A: N.41, S.52, T.53, L.54, W.102, P.105, M.108 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.102, A:W.102 Hydrogen bonds: A:T.53

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

SO4.3: 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 SO4.4: 1 residues within 4Å: Chain A: K.21 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.18 Water bridges: A:K.21 Salt bridges: A:K.21 SO4.5: 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 SO4.6: 3 residues within 4Å: Chain A: R.78, R.149, D.150 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:D.150, A:D.150 Salt bridges: A:R.78, A:R.149

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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