SMTL ID : 6t0d.2 (1 other biounit)

Crystal structure of YTHDC1 with fragment 27 (DHU_DC1_256)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

monomer

Ligands

1 x M4N: ~{N}-methyl-3-phenyl-1~{H}-pyrazole-5-carboxamide(Non-covalent)

M4N.1: 11 residues within 4Å: Chain A: K.35, N.37, N.41, W.51, S.52, L.54, R.78, W.102, L.113, D.150 Ligands: SO4.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.54, A:D.150 Hydrogen bonds: A:N.41, A:S.52, A:S.52 Water bridges: A:R.78 pi-Cation interactions: A:R.78

5 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: 1 residues within 4Å: Chain A: K.60 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.60 Salt bridges: A:K.60 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: 4 residues within 4Å: Chain A: R.78, R.149, D.150 Ligands: M4N.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:R.78, A:R.78 Salt bridges: A:R.78 SO4.6: 3 residues within 4Å: Chain A: S.93, H.94, H.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.95 Water bridges: A:E.92, A:S.93, A:S.93

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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