SMTL ID : 9dg6.1

Tetrahydroprotoberberine N-methyltransferase complex with N-methylcanadine and SAH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 21 residues within 4Å: Chain A: I.98, Y.106, K.122, Q.123, S.124, G.162, C.163, G.164, L.184, T.185, N.186, Q.190, A.211, D.212, V.213, I.228, E.229, T.230, H.233, M.234 Ligands: 01.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Q.123, A:S.124, A:G.162, A:G.162, A:G.164, A:T.185, A:N.186, A:N.186, A:Q.190, A:D.212, A:V.213 Water bridges: A:I.228 Salt bridges: A:K.122 SAH.4: 21 residues within 4Å: Chain B: I.98, Y.106, K.122, Q.123, S.124, G.162, C.163, G.164, L.184, T.185, N.186, Q.190, A.211, D.212, V.213, I.228, E.229, T.230, H.233, M.234 Ligands: 01.5 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Q.123, B:S.124, B:G.162, B:G.162, B:G.164, B:N.186, B:N.186, B:Q.190, B:D.212, B:D.212, B:V.213 Water bridges: B:I.228 Salt bridges: B:K.122

2 x 01: (S)-cis-N-methylcanadine

01.2: 19 residues within 4Å: Chain A: M.101, T.105, Y.106, F.117, Q.123, S.124, E.229, E.232, H.233, I.259, F.268, F.282, V.287, M.315, W.322, F.357, Q.364, F.365 Ligands: SAH.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.117, A:Q.123, A:E.232, A:I.259, A:F.282, A:V.287, A:W.322, A:F.357 Hydrogen bonds: A:Q.123 Salt bridges: A:E.232 01.5: 19 residues within 4Å: Chain B: M.101, T.105, Y.106, F.117, Q.123, S.124, E.229, E.232, H.233, I.259, F.268, F.282, V.287, M.315, W.322, F.357, Q.364, F.365 Ligands: SAH.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.117, B:Q.123, B:E.232, B:I.259, B:F.282, B:V.287, B:W.322, B:F.357 Hydrogen bonds: B:Q.123 Salt bridges: B:E.232

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 8 residues within 4Å: Chain A: F.63, R.66, H.266, H.267, F.268, E.269, D.275, S.278 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.269, A:S.278 Salt bridges: A:R.66, A:H.266 SO4.6: 8 residues within 4Å: Chain B: F.63, R.66, H.266, H.267, F.268, E.269, D.275, S.278 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.269, B:S.278 Salt bridges: B:R.66, B:H.266

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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