SMTL ID : 6t0x.1 (1 other biounit)

Crystal structure of YTHDC1 with fragment 22 (ACA_DC1_001)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

monomer

Ligands

1 x M6W: (3~{S})-~{N}-methylpyrrolidine-3-carboxamide(Non-covalent)

M6W.1: 6 residues within 4Å: Chain A: K.35, N.41, W.51, S.52, W.102, D.150 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.41, A:S.52, A:D.150 Water bridges: A:R.78

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

SO4.2: 4 residues within 4Å: Chain A: G.18, T.19, S.20, K.21 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.18, A:S.20, A:K.21 Water bridges: A:G.18, A:T.19, A:S.20 Salt bridges: A:K.21 SO4.3: 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 SO4.4: 3 residues within 4Å: Chain A: S.93, H.94, H.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.95 Salt bridges: A:H.94, A:H.95 SO4.5: 3 residues within 4Å: Chain A: W.139, Q.152, E.153 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.152, A:E.153 Water bridges: A:K.60, A:K.60, A:K.60, A:K.60, A:K.60, A:Q.152, A:Q.152, A:E.153, A:E.153 Salt bridges: A:K.60

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
A

YTHDC1

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