SMTL ID : 6t07.2 (1 other biounit)

Crystal structure of YTHDC1 with fragment 20 (DHU_DC1_134)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x M45: ~{N}-[(2~{S})-pyrrolidin-2-yl]-1~{H}-1,2,4-triazol-5-amine(Non-covalent)

M45.1: 10 residues within 4Å: Chain A: N.41, W.51, S.52, T.53, L.54, W.102, M.108, L.113, D.150 Ligands: SO4.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.41, A:W.51, A:W.102 Hydrogen bonds: A:S.52, A:L.54

6 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: 4 residues within 4Å: Chain A: K.60, G.151, Q.152, E.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.153 Water bridges: A:K.60 Salt bridges: A:K.60 SO4.4: 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, A:H.95 Salt bridges: A:H.94 SO4.5: 3 residues within 4Å: Chain A: R.78, R.149, D.150 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.150 Water bridges: A:D.150 Salt bridges: A:R.78, A:R.149 SO4.6: 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 SO4.7: 5 residues within 4Å: Chain A: S.36, N.37, N.41, P.105 Ligands: M45.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.37, A:N.37, A:N.41

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

YTH domain-containing protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

YTH domain-containing protein 1

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