SMTL ID : 6t09.1 (1 other biounit)

Crystal structure of YTHDC1 with fragment 24 (PSI_DC1_003)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x M4T: ~{N}-pyridin-3-ylethanamide(Non-covalent)

M4T.1: 10 residues within 4Å: Chain A: N.41, W.51, S.52, T.53, L.54, W.102, L.104, P.105, L.113, D.150 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.51, A:W.102, A:L.104, A:L.113 Hydrogen bonds: A:N.41, A:S.52, A:L.54 Water bridges: A:T.53

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

SO4.2: 4 residues within 4Å: Chain A: G.18, T.19, S.20, K.21 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.18, A:S.20, A:S.20, A:K.21 Water bridges: A:L.22 Salt bridges: A:K.21 SO4.3: 3 residues within 4Å: Chain A: W.139, Q.152, E.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.151, A:Q.152, A:E.153 Water bridges: A:W.139 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 Salt bridges: A:H.94, A:H.95 SO4.5: 1 residues within 4Å: Chain A: P.99 No protein-ligand interaction detected (PLIP) SO4.6: 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:R.78, A:R.78 Salt bridges: A:R.78

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

Related Entries With Identical Sequence