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

Crystal structure of YTHDC1 with fragment 12 (DHU_DC1_150)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x M5N: 4-propan-2-yl-5,6,7,8-tetrahydro-4~{a}~{H}-quinazolin-2-one(Non-covalent)

M5N.1: 11 residues within 4Å: Chain A: N.41, W.51, S.52, T.53, L.54, W.102, V.103, P.105, M.108, L.113, D.150 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:N.41, A:W.51, A:L.54, A:L.54, A:W.102, A:W.102, A:L.113, A:L.113 Hydrogen bonds: A:N.41

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

SO4.2: 2 residues within 4Å: Chain A: R.125, E.126 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.126 Water bridges: A:R.125, A:R.125, A:R.125 Salt bridges: A:R.125 SO4.3: 3 residues within 4Å: Chain A: K.60, 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

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
B

YTHDC1

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