SMTL ID : 7ltr.2 (1 other biounit)

Structure of the heteromeric complex between the alpha-N-methyltransferase (SonM) and a truncated construct of the RiPP precursor (SonA) (with SAM)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-2-2-mer

Ligands

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

SAM.1: 19 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, N.210, P.233, I.234, S.235, T.236 Ligands: GOL.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.166 Hydrogen bonds: A:Y.93, A:H.95, A:A.125, A:Q.167, A:A.208, A:A.208, A:N.210, A:S.235, A:T.236 Water bridges: A:Q.167, A:A.169, A:S.235

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: L.34, Y.58, Y.71, Y.93, A.100, C.101, V.102 Ligands: SAM.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.58, A:Y.93, A:C.101, A:V.102 Water bridges: A:Y.58, A:Y.93 GOL.3: 8 residues within 4Å: Chain A: H.95, V.98, S.124, E.126, A.127 Chain C: E.126, A.127, W.130 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain A Water bridges: C:S.124, C:S.124, C:H.142, A:S.124, A:S.124 Hydrogen bonds: A:S.124, A:E.126, A:A.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, F.S. et al., Conformational rearrangements enable iterative backbone N-methylation in RiPP biosynthesis. Nat Commun (2021)

Release Date

2021-09-29

Peptides

TP-methylase family protein: AC
LigA domain-containing protein: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

C
J

B
I

D
K

TP-methylase family protein

LigA domain-containing protein

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