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

Crystal structure of YTHDC1 with fragment 10 (DHU_DC1_076)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x M4Q: 6-[[methyl(thiophen-3-ylmethyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione(Non-covalent)

M4Q.1: 15 residues within 4Å: Chain A: K.35, S.36, N.37, N.41, W.51, S.52, T.53, L.54, R.78, W.102, L.104, P.105, M.108, L.113, D.150 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.51, A:L.113 Hydrogen bonds: A:N.37, A:R.78, A:R.78, A:D.150 Water bridges: A:L.54, A:N.57, A:D.150, A:D.150

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

SO4.2: 4 residues within 4Å: Chain A: K.35, R.78, R.149, D.150 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:G.148, A:D.150 Salt bridges: A:R.78 SO4.3: 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:T.19, A:S.20, A:S.20 Salt bridges: A:K.21 SO4.4: 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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