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

Crystal structure of YTHDC1 with fragment 11 (DHU_DC1_128)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.17 Å

Oligo State

monomer

Ligands

1 x M4K: 6-[[cyclopropyl-(phenylmethyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione(Non-covalent)

M4K.1: 16 residues within 4Å: Chain A: I.34, 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.54, A:W.102, A:P.105, A:L.113 Hydrogen bonds: A:R.78, A:D.150 Water bridges: A:L.54, A:D.150, A:D.150

3 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.35, R.78, R.149, D.150 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:R.78, A:R.78, A:R.149 Salt bridges: A:K.35, A:R.78, A:R.149 SO4.4: 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:H.95 Salt bridges: A:H.94, A:H.95

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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