SMTL ID : 6ym2.1 (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: 12 residues within 4Å: Chain A: K.35, S.36, N.37, N.41, W.51, S.52, R.78, W.102, P.105, L.113, D.150 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.37, A:N.41, A:S.52

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

SO4.2: 4 residues within 4Å: Chain A: G.18, T.19, S.20, K.21 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.18, A:T.19, A:S.20, A:S.20, A:K.21 Water bridges: A:K.21, A:K.21 Salt bridges: A:K.21 SO4.3: 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 Water bridges: A:H.95 Salt bridges: A:H.94 SO4.4: 4 residues within 4Å: Chain A: R.78, R.149, D.150 Ligands: OYK.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.150 Salt bridges: A:R.78 SO4.5: 3 residues within 4Å: Chain A: W.139, Q.152, E.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.152, A:E.153 Water bridges: A:Q.152 Salt bridges: A:K.60 SO4.6: 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

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
A

YTHDC1

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