SMTL ID : 6we9.2 (1 other biounit)

YTH domain of human YTHDC1 with 11mer ssDNA Containing N6mA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

7 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: EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.22, A:K.29 Water bridges: A:K.29 EDO.2: 3 residues within 4Å: Chain A: S.76, H.77, H.78 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.78, A:H.78 EDO.4: 6 residues within 4Å: Chain A: H.22, S.63, K.65, Q.67, E.109 Ligands: EDO.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.67, A:E.109 EDO.5: 2 residues within 4Å: Chain A: R.61, R.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.61, A:R.132, A:R.132 EDO.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain A: F.48, R.49, A.51 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.51 EDO.10: 2 residues within 4Å: Chain A: W.122, E.138 No protein-ligand interaction detected (PLIP)

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

SO4.3: 3 residues within 4Å: Chain A: N.20, P.88, A.89 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.20, A:A.89 Water bridges: A:N.20

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: K.43, R.132, D.133, G.134, Q.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.43, A:G.134 GOL.9: 7 residues within 4Å: Chain A: H.117, L.118, T.119, P.121, E.138, E.140, C.141 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.117, A:T.119, A:E.138, A:C.141

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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