SMTL ID : 6t0o.1 (1 other biounit)

Crystal structure of YTHDC1 with fragment 14 (ACA_DC1_004)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

monomer

Ligands

1 x M6N: 2-methyl-3~{H}-pyrido[3,4-d]pyrimidin-4-one(Non-covalent)

M6N.1: 13 residues within 4Å: Chain A: K.35, S.36, N.37, N.41, W.51, S.52, T.53, L.54, W.102, P.105, M.108, L.113, D.150 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.51, A:W.102 Hydrogen bonds: A:N.37, A:N.41, A:S.52, A:T.53, A:L.54

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

SO4.2: 4 residues within 4Å: Chain A: G.18, T.19, S.20, K.21 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.18, A:G.18, A:S.20, A:K.21 Water bridges: A:S.20, A:L.22 Salt bridges: A:K.21 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 SO4.4: 4 residues within 4Å: Chain A: S.90, S.91, E.92, H.94 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.92, A:E.92, A:E.92 Salt bridges: A:H.94 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.94, A:H.94 Salt bridges: A:H.94 SO4.6: 2 residues within 4Å: Chain A: S.98, P.99 No protein-ligand interaction detected (PLIP) SO4.7: 4 residues within 4Å: Chain A: K.60, W.139, Q.152, E.153 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.152, A:E.153 Water bridges: A:E.153, A:E.153 Salt bridges: A:K.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bedi, R.K. et al., Selectively Disrupting m6A-Dependent Protein-RNA Interactions with Fragments. Acs Chem.Biol. (2020)

Release Date

2020-03-04

Peptides

YTHDC1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

YTHDC1

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