SMTL ID : 6t03.1 (1 other biounit)

Crystal structure of YTHDC1 with fragment 16 (DHU_DC1_017)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: G.18, T.19, S.20, K.21 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.18, A:S.20, A:K.21 Water bridges: A:G.18, A:G.18, A:G.18, A:T.19, A:S.20, A:L.22 Salt bridges: A:K.21 SO4.2: 3 residues within 4Å: Chain A: W.139, Q.152, E.153 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.152, A:E.153 Water bridges: A:K.60, A:W.139, A:Q.152, A:Q.152 SO4.3: 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.95

1 x MZY: 1,3-dihydroimidazole-2-thione(Non-covalent)

MZY.4: 5 residues within 4Å: Chain A: N.41, W.51, S.52, W.102, L.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.52 Water bridges: A:N.41 pi-Stacking: A:W.102, A:W.102

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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