SMTL ID : 6zd5.2 (1 other biounit)

Crystal structure of YTHDC1 S378A mutant complex with m6A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: G.18, T.19, S.20, K.21 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.18, A:G.18, A:S.20, A:K.21 Water bridges: A:L.22 Salt bridges: A:K.21 SO4.2: 5 residues within 4Å: Chain A: K.60, W.139, G.151, Q.152, E.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.153 Water bridges: A:Q.152, A:Q.152 Salt bridges: A:K.60

1 x 6MD: N-methyladenosine(Non-covalent)

6MD.3: 12 residues within 4Å: Chain A: K.35, S.36, N.37, N.41, W.51, A.52, T.53, R.78, W.102, M.108, L.113, D.150 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.37, A:N.41, A:A.52, A:R.78 Water bridges: A:D.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Atomistic and Thermodynamic Analysis of N6-Methyladenosine (m 6 A) Recognition by the Reader Domain of YTHDC1. J Chem Theory Comput (2021)

Release Date

2021-01-13

Peptides

YTH domain containing 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

YTH domain containing 1

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