SMTL ID : 6t12.2 (1 other biounit)

Crystal structure of YTHDC1 with fragment 30 (DHU_DC1_220)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

monomer

Ligands

1 x M78: ~{N},2,3-trimethyl-1~{H}-indole-5-carboxamide(Non-covalent)

M78.1: 12 residues within 4Å: Chain A: N.41, W.51, S.52, T.53, L.54, W.102, V.103, P.105, M.108, L.113, D.150 Ligands: SO4.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.54, A:W.102, A:L.113, A:L.113 Hydrogen bonds: A:S.52 Water bridges: A:D.150

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

SO4.2: 2 residues within 4Å: Chain A: R.125, E.126 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.126 Water bridges: A:R.125, A:R.125 Salt bridges: A:R.125 SO4.3: 4 residues within 4Å: Chain A: R.78, R.149, D.150 Ligands: M78.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:K.35, A:R.78, A:R.78, A:R.78, A:R.149, A:D.150, A:D.150 Salt bridges: A:R.78, A:R.149 SO4.4: 2 residues within 4Å: Chain A: G.18, K.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.18 Salt bridges: A:K.21 SO4.5: 1 residues within 4Å: Chain A: R.125 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.125, A:R.125, A:E.170 Salt bridges: A:R.125

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

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