SMTL ID : 6wea.1 (3 other biounits)

YTH domain of human YTHDC1 with a 10mer Oligo Containing N6mA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: H.22, V.25, S.26, K.29, Q.67 Ligands: NA.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.22, A:K.29 Water bridges: A:S.26, A:K.29, A:E.109 EDO.5: 5 residues within 4Å: Chain A: H.117, L.118, T.119, E.140, C.141 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.117, A:T.119 Water bridges: A:T.119, A:C.141 EDO.8: 3 residues within 4Å: Chain A: P.121, W.122, E.138 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: N.123, E.124, K.126 Chain B: C.7 Ligands: SO4.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.123, A:E.124 Water bridges: A:K.126 EDO.10: 5 residues within 4Å: Chain A: H.22, S.63, K.65, Q.67, E.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.67 EDO.11: 1 residues within 4Å: Chain A: D.156 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.156

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

SO4.2: 3 residues within 4Å: Chain A: N.20, P.88, A.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.20, A:A.89 SO4.3: 1 residues within 4Å: Chain A: K.114 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.114 SO4.4: 3 residues within 4Å: Chain A: R.61, R.132 Chain B: C.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.61 Water bridges: A:R.132 Salt bridges: A:R.132 SO4.6: 2 residues within 4Å: Chain A: R.108, P.150 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.109 Salt bridges: A:R.108 SO4.7: 3 residues within 4Å: Chain A: T.2, S.3, K.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.2, A:S.3, A:K.4 Water bridges: A:S.3, A:S.3, A:L.5 Salt bridges: A:K.4 SO4.13: 3 residues within 4Å: Chain A: K.126 Chain B: C.7 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.126, A:R.132 Salt bridges: A:K.126

1 x NA: SODIUM ION(Non-functional Binders)

NA.12: 2 residues within 4Å: Chain A: S.26 Ligands: EDO.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Woodcock, C.B. et al., Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA. Nucleic Acids Res. (2020)

Release Date

2020-07-15

Peptides

YTH domain-containing protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

YTH domain-containing protein 1

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