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

Crystal structure of S. pombe Dnmt2 methyltransferase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 17 residues within 4Å: Chain A: Y.17, S.18, G.19, I.20, G.21, G.22, D.41, I.42, N.43, M.61, D.62, I.63, S.82, A.104, N.314, S.315, I.316 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.17, A:I.20, A:G.21, A:G.22, A:I.42, A:N.43, A:D.62, A:I.63, A:S.82, A:I.316 Water bridges: A:M.23, A:M.23 pi-Stacking: A:Y.17, A:Y.17

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: Q.228, F.229, D.230, C.240, V.250, Q.251, G.252, A.253, G.254 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.228, A:D.230, A:V.250, A:G.252, A:A.253, A:G.254 Water bridges: A:C.241, A:G.252 GOL.3: 3 residues within 4Å: Chain A: L.29, N.31, K.319 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.31, A:K.319, A:K.319 GOL.4: 4 residues within 4Å: Chain A: W.225, Q.228, V.250, Q.251 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.225, A:Q.228, A:V.250, A:Q.251 GOL.5: 3 residues within 4Å: Chain A: E.219, S.220, N.223 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.223 Water bridges: A:S.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johannsson, S. et al., Structural insights into the stimulation of S. pombe Dnmt2 catalytic efficiency by the tRNA nucleoside queuosine. Sci Rep (2018)

Release Date

2018-06-20

Peptides

tRNA (cytosine(38)-C(5))-methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

tRNA (cytosine(38)-C(5))-methyltransferase

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