SMTL ID : 6ym8.2 (1 other biounit)

Crystal structure of YTHDC1 with compound YLI_DC1_002

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x OYN: 2-chloranyl-~{N}-methyl-9~{H}-purin-6-amine(Non-covalent)

OYN.1: 13 residues within 4Å: Chain A: K.35, S.36, N.37, N.38, N.41, W.51, S.52, T.53, W.102, P.105, M.108, L.113, D.150 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.37, A:N.41, A:S.52 Water bridges: A:K.35, A:K.35, A:N.37, A:N.37

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

SO4.2: 2 residues within 4Å: Chain A: R.125, E.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.126 Water bridges: A:R.125 Salt bridges: A:R.125 SO4.3: 2 residues within 4Å: Chain A: G.18, K.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.18 Salt bridges: A:K.21 SO4.4: 2 residues within 4Å: Chain A: R.149, D.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:K.35, A:N.57 SO4.5: 3 residues within 4Å: Chain A: S.93, H.94, H.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.95 Water bridges: A:H.95 Salt bridges: A:H.94, A:H.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bedi, R.K. et al., Crystal structure of YTHDC1 with compound YLI_DC1_002. 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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