SMTL ID : 6t10.1 (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: 12 residues within 4Å: Chain A: N.37, N.41, W.51, S.52, T.53, L.54, W.102, P.105, M.108, M.112, L.113, D.150 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.54 Hydrogen bonds: A:S.52, A:L.54, A:D.150 Water bridges: A:N.41, A:N.41, A:N.41, A:D.150, A:D.150

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

SO4.2: 2 residues within 4Å: Chain A: 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 SO4.3: 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

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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