SMTL ID : 6t08.1 (1 other biounit)

Crystal structure of YTHDC1 with fragment 21 (DHU_DC1_131)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

monomer

Ligands

1 x M5B: ~{N}-(1~{H}-imidazol-2-yl)thiophene-2-sulfonamide(Non-covalent)

M5B.1: 13 residues within 4Å: Chain A: K.35, S.36, N.37, N.38, N.41, W.51, S.52, R.78, W.102, L.104, P.105, M.108, D.150 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:N.41, A:W.51, A:W.102 Hydrogen bonds: A:K.35, A:K.35, A:N.37, A:N.38, A:N.41, A:R.78 Water bridges: A:T.53, A:T.53

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

SO4.2: 4 residues within 4Å: Chain A: G.18, T.19, S.20, K.21 9 PLIP interactions: 9 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, A:K.21, A:L.22 Salt bridges: A:K.21 SO4.3: 5 residues within 4Å: Chain A: K.60, W.139, G.151, Q.152, E.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.152, A:E.153 Water bridges: A:Q.152 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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