SMTL ID : 6we8.3 (2 other biounits)

YTH domain of human YTHDC1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.18 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.108, E.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.109 Water bridges: A:R.108 Salt bridges: A:R.108 SO4.2: 2 residues within 4Å: Chain A: G.1, K.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.1 Salt bridges: A:K.4 SO4.3: 3 residues within 4Å: Chain A: S.76, H.77, H.78 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.78 Water bridges: A:H.78 Salt bridges: A:H.77, A:H.78 SO4.4: 3 residues within 4Å: Chain A: R.61, R.132, D.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.133 Water bridges: A:D.133 Salt bridges: A:R.61 SO4.11: 3 residues within 4Å: Chain B: S.76, H.77, H.78 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.78 Water bridges: B:S.76, B:H.78 Salt bridges: B:H.77 SO4.13: 7 residues within 4Å: Chain A: K.43, G.134, Q.135, E.136 Chain B: G.1, S.3, K.4 14 PLIP interactions: 6 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:G.1, B:S.3, B:K.4, A:Q.135, A:Q.135, A:E.136 Water bridges: B:T.2, B:T.2, A:K.43, A:K.43, A:K.43, A:K.43 Salt bridges: B:K.4, A:K.43

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

EDO.5: 2 residues within 4Å: Chain A: K.42, N.45 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.42, A:N.45 Water bridges: A:E.41, A:E.41 EDO.6: 4 residues within 4Å: Chain A: H.22, R.61, E.62, S.63 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.63 EDO.7: 3 residues within 4Å: Chain A: G.64, F.112, K.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.64, A:K.129 EDO.8: 4 residues within 4Å: Chain A: W.34, S.35, T.36, L.96 6 PLIP interactions: 6 interactions with chain A Water bridges: A:N.24, A:W.34, A:T.36, A:T.36, A:L.37, A:D.133 EDO.9: 6 residues within 4Å: Chain A: H.22, V.25, S.26, K.29, V.60, Q.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.22, A:K.29 EDO.12: 4 residues within 4Å: Chain B: K.29, R.107, R.108, E.109 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.29, B:R.107 Water bridges: B:R.108, B:R.108 EDO.14: 3 residues within 4Å: Chain B: F.48, A.51, R.52 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.51 EDO.15: 5 residues within 4Å: Chain B: S.19, N.24, W.34, S.35, W.85 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.24 Water bridges: B:N.21

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 2 residues within 4Å: Chain B: A.116, H.117 No protein-ligand interaction detected (PLIP)

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

YTH domain-containing protein 1

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