SMTL ID : 9chk.1

Structure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA-Y62A) heteromeric complex (bound to SAM)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-2-2-mer

Ligands

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

SAM.1: 18 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 Ligands: GOL.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.93, A:H.95, A:H.95, 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 SAM.3: 18 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 Ligands: GOL.4 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:Y.93, C:H.95, 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

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: L.34, Y.58, L.92, Y.93, A.100 Ligands: SAM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.58 GOL.4: 7 residues within 4Å: Chain C: L.34, Y.71, Y.93, A.100, C.101, V.102 Ligands: SAM.3 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.71, C:Y.71, C:Y.93, C:Y.93, C:C.101, C:V.102

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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