SMTL ID : 6ym2.2 (1 other biounit)

Crystal structure of YTHDC1 with compound ADO_AC_25

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x OYK: ~{N},9-dimethylpurin-6-amine(Non-covalent)

OYK.1: 13 residues within 4Å: Chain A: K.35, S.36, N.37, N.41, W.51, S.52, R.78, W.102, P.105, M.108, L.113, D.150 Ligands: SO4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.37, A:N.41, A:S.52

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

SO4.2: 4 residues within 4Å: Chain A: R.78, R.149, D.150 Ligands: OYK.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:R.78, A:D.150 Salt bridges: A:R.78, A:R.149 SO4.3: 2 residues within 4Å: Chain A: R.125, E.126 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.126 Water bridges: A:R.125, A:R.125, A:R.125, A:R.125 Salt bridges: A:R.125 SO4.4: 4 residues within 4Å: Chain A: K.35, K.146, I.147, G.148 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.148 Water bridges: A:K.35, A:K.35, A:K.35, A:K.35, A:R.78 Salt bridges: A:K.35 SO4.5: 3 residues within 4Å: Chain A: S.93, H.94, H.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.95 Salt bridges: A:H.94 SO4.6: 1 residues within 4Å: Chain A: E.79 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.79, A:E.79 Water bridges: A:G.81, A:G.81, A:K.146, A:K.146 SO4.7: 3 residues within 4Å: Chain A: K.59, N.62, R.66 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.62 Salt bridges: A:K.59, A:R.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bedi, R.K. et al., Crystal structure of YTHDC1 with compound ADO_AC_25. To Be Published

Release Date

2021-04-14

Peptides

YTHDC1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

YTHDC1

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