SMTL ID : 7vvw.1

MmtN-SAM complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-trimer

Ligands

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

SAM.1: 17 residues within 4Å: Chain A: W.24, V.45, G.46, G.48, D.69, L.70, L.74, V.100, S.101, L.102, C.121, P.123, E.127, V.131, A.135, W.162, L.177 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.131 Hydrogen bonds: A:L.70, A:S.101, A:L.102, A:L.122 Water bridges: A:G.46 SAM.2: 18 residues within 4Å: Chain B: W.24, V.45, G.46, G.48, D.69, L.70, V.100, S.101, L.102, C.121, L.122, P.123, Q.124, E.127, P.128, V.131, Y.159, P.161 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.48, B:L.70, B:S.101, B:L.102, B:L.122, B:Q.124, B:Y.159 SAM.5: 15 residues within 4Å: Chain C: W.24, T.25, V.45, G.46, G.48, D.69, L.70, L.74, V.100, S.101, L.102, C.121, P.123, P.128, V.131 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.25, C:L.70, C:S.101, C:L.102

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain B: L.249 Chain C: Q.124, V.125, G.126 Ligands: GOL.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.126 GOL.4: 6 residues within 4Å: Chain C: P.123, E.127, R.132, Y.160, W.162 Ligands: GOL.3 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.127, C:R.132, C:Y.160

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 6 residues within 4Å: Chain A: P.169, R.183 Chain B: P.169, R.183 Chain C: P.169, R.183 8 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A, 2 interactions with chain C Water bridges: B:E.179, B:R.183, B:R.183, A:E.179, C:R.183 Salt bridges: B:R.183, A:R.183, C:R.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peng, M. et al., Insights into methionine S-methylation in diverse organisms. Nat Commun (2022)

Release Date

2022-04-20

Peptides

SAM-dependent methyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

SAM-dependent methyltransferase

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