SMTL ID : 6t10.2 (1 other biounit)

Crystal structure of YTHDC1 with fragment 28 (DHU_DC1_176)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

1 x M6Z: 5-iodanyl-~{N}-methyl-1~{H}-indazole-3-carboxamide(Non-covalent)

M6Z.1: 9 residues within 4Å: Chain A: N.41, W.51, S.52, T.53, L.54, R.78, W.102, L.104, D.150 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.54, A:L.104 Hydrogen bonds: A:N.41, A:S.52, A:D.150 Water bridges: A:D.150

5 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: 4 residues within 4Å: Chain A: K.60, 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:K.60 Salt bridges: A:K.60 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: 2 residues within 4Å: Chain A: G.18, K.21 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.18 Water bridges: A:G.18 Salt bridges: A:K.21 SO4.6: 3 residues within 4Å: Chain A: R.78, R.149, D.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:D.150 Salt bridges: A:R.78

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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