SMTL ID : 9mg4.1

Structure of Saccharomyces cerevisiae mRNA cap (guanine-N7) methyltransferase, Abd1, in complex with SAH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

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

SAH.1: 16 residues within 4Å: Chain A: K.15, G.33, C.34, G.35, D.39, D.55, I.56, S.57, G.83, D.84, C.85, F.86, Q.110, F.111, C.112, Y.115 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.33, A:G.35, A:I.56, A:D.84, A:D.84, A:C.85, A:F.86, A:Q.110 Water bridges: A:K.15, A:K.15, A:K.15, A:E.31, A:E.31, A:S.60, A:S.60, A:G.87 Salt bridges: A:K.15

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

EDO.2: 5 residues within 4Å: Chain A: G.91, V.94, F.102, K.132, S.133 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.132 EDO.3: 5 residues within 4Å: Chain A: N.155, K.156, F.157, P.158, Y.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.157, A:Y.185 EDO.4: 3 residues within 4Å: Chain A: H.139, V.228, R.283 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 4 residues within 4Å: Chain A: N.11, F.111, L.199, A.202 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.111 Hydrogen bonds: A:N.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nilson, D.J. et al., Structural basis for sensitivity and acquired resistance of fungal cap guanine-N7 methyltransferases to the antifungal antibiotic sinefungin. Nucleic Acids Res. (2025)

Release Date

2025-07-09

Peptides

mRNA cap guanine-N7 methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

mRNA cap guanine-N7 methyltransferase