SMTL ID : 8t1t.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-2-2-mer

Ligands

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

SAM.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 16 PLIP interactions: 16 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:Y.93, A:Q.167, A:Q.167, A:A.169, A:N.210, A:P.233, A:S.235 SAM.2: 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 13 PLIP interactions: 13 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 Water bridges: C:Y.93, C:Q.167, C:A.169, C:N.210, C:P.233, C:S.235

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 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Metal complexes: C:E.126, C:H.142, A:E.126, A:H.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crone, K.K. et al., RiPP enzyme heterocomplex structure-guided discovery of a bacterial borosin alpha- N -methylated peptide natural product. Rsc Chem Biol (2023)

Release Date

2023-11-22

Peptides

Alpha-N-methyltransferase (SonM): AC
RiPP precursor (SonA): BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Alpha-N-methyltransferase (SonM)

RiPP precursor (SonA)

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