SMTL ID : 9dgb.1

Tetrahydroprotoberberine N-methyltransferase in complex with (S)-reticuline and SAM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

SAM.1: 18 residues within 4Å: Chain A: K.122, Q.123, S.124, G.162, C.163, G.164, L.184, N.186, Q.190, A.211, D.212, V.213, I.228, E.229, T.230, H.233, M.234 Ligands: REN.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Q.123, A:S.124, A:G.162, A:G.164, A:N.186, A:N.186, A:Q.190, A:D.212, A:V.213, A:K.235 Water bridges: A:Q.123, A:G.167, A:T.185, A:I.228 Salt bridges: A:K.122 SAM.4: 18 residues within 4Å: Chain B: K.122, Q.123, S.124, G.162, C.163, G.164, L.184, N.186, Q.190, A.211, D.212, V.213, I.228, E.229, T.230, H.233, M.234 Ligands: REN.5 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Q.123, B:S.124, B:G.162, B:G.164, B:N.186, B:N.186, B:Q.190, B:D.212, B:D.212, B:V.213, B:K.235 Water bridges: B:Q.123, B:G.167, B:I.228 Salt bridges: B:K.122

2 x REN: (S)-reticuline(Non-covalent)

REN.2: 12 residues within 4Å: Chain A: F.117, Q.123, E.229, I.259, F.268, F.282, I.289, W.322, F.357, Q.364, F.365 Ligands: SAM.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.117, A:Q.123, A:I.259, A:F.282, A:W.322, A:F.357, A:F.357 Water bridges: A:Y.277 Salt bridges: A:E.229 REN.5: 12 residues within 4Å: Chain B: F.117, Q.123, E.229, I.259, F.268, F.282, I.289, W.322, F.357, Q.364, F.365 Ligands: SAM.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.117, B:Q.123, B:I.259, B:F.282, B:W.322, B:F.357, B:F.357 Salt bridges: B:E.229

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain A: G.125, C.126, Y.127, S.142, Y.146, E.229, D.257, H.314, M.315, V.375, Q.377 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.146, A:D.257, A:Q.377 Water bridges: A:H.314 GOL.6: 11 residues within 4Å: Chain B: G.125, C.126, Y.127, S.142, Y.146, E.229, D.257, H.314, M.315, V.375, Q.377 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.229, B:D.257, B:Q.377 Water bridges: B:H.314

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lang, D.E. et al., The stereospecific activities of the tetrahydroprotoberberine N-methyltransferase with alternative substrates provide insight into the catalytic mechanisms of benzylisoquinoline alkaloid N-methylation. To Be Published

Release Date

2025-09-17

Peptides

Tetrahydroprotoberberine N-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Tetrahydroprotoberberine N-methyltransferase

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