SMTL ID : 6zcn.1 (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: 3 residues within 4Å: Chain A: N.37, P.105, A.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.37, A:A.106 Water bridges: A:L.104 SO4.2: 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:S.20, A:K.21 Water bridges: A:G.18, A:L.22 Salt bridges: A:K.21 SO4.3: 3 residues within 4Å: Chain A: W.139, Q.152, E.153 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.152, A:E.153 Water bridges: A:Q.152, A:E.153, A:E.153 Salt bridges: A:K.60

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

6MZ.4: 13 residues within 4Å: Chain A: K.35, S.36, N.37, N.41, W.51, S.52, L.54, R.78, W.102, P.105, M.108, L.113, D.150 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.35, A:N.37, A:N.41, A:S.52, A:R.78 Water bridges: A:T.53, 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
A

YTHDC1

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