SMTL ID : 6t11.2 (1 other biounit)

Crystal structure of YTHDC1 with fragment 29 (DHU_DC1_218)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

monomer

Ligands

1 x O2A: N-methyl-1H-indole-7-carboxamide(Non-covalent)

O2A.1: 12 residues within 4Å: Chain A: N.41, W.51, S.52, T.53, L.54, W.102, V.103, L.104, P.105, M.108, L.113, D.150 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.102, A:P.105, A:L.113, A:L.113 Hydrogen bonds: A:S.52, A:L.54, A:D.150 Water bridges: A:N.41 pi-Stacking: A:W.102, A:W.102

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

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

YTHDC1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

YTHDC1

Related Entries With Identical Sequence