SMTL ID : 9ch1.1

Structure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA-I65W) heteromeric complex (bound to SAM)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

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

SAH.1: 17 residues within 4Å: Chain A: L.11, Y.93, G.94, H.95, V.98, F.99, S.124, A.125, W.166, Q.167, Y.206, E.207, A.208, P.233, I.234, S.235, T.236 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:H.95, A:V.98, A:A.125, A:Q.167, A:A.208, A:A.208, A:S.235, A:T.236 Water bridges: A:N.210, A:S.235

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: Y.58, Y.71, Y.93 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.71, A:Y.93, A:Y.93 GOL.5: 2 residues within 4Å: Chain C: Y.58, Y.93 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.58, C:Y.93

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: E.126, H.142 Chain C: E.126, H.142 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Metal complexes: A:E.126, A:E.126, A:H.142, C:E.126, C:H.142

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.4: 17 residues within 4Å: Chain C: L.11, Y.93, G.94, H.95, V.98, F.99, S.124, A.125, W.166, Q.167, Y.206, E.207, A.208, P.233, I.234, S.235, T.236 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Y.93, C:H.95, C:A.125, C:Q.167, C:A.208, C:A.208, C:S.235, C:T.236 Water bridges: C:N.210, C:S.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crone, K.K. et al., alpha-N-Methyltransferase regiospecificity is mediated by proximal, redundant enzyme-substrate interactions. Protein Sci. (2025)

Release Date

2025-01-29

Peptides

TP-methylase family protein: AC
Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

TP-methylase family protein

Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein

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