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

Crystal structure of YTHDC1 with m6A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

SO4.1: 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 SO4.2: 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 SO4.3: 3 residues within 4Å: Chain A: N.37, P.105, A.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.37, A:A.106

1 x 6MZ: N6-METHYLADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

6MZ.4: 12 residues within 4Å: Chain A: K.35, S.36, N.37, N.41, W.51, S.52, L.54, W.102, P.105, M.108, L.113, D.150 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.35, A:N.37, A:N.41, A:S.52 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

2020-07-29

Peptides

YTHDC1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

YTHDC1

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