SMTL ID : 8xdr.1

O-methyltransferase from Lycoris aurea complexed with Mg, SAH, and 3,4-dihydroxybenzaldehyde

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.158, K.161, D.184, N.185 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.158, A:D.184, H2O.1, H2O.3, H2O.5 MG.6: 5 residues within 4Å: Chain B: D.158, K.161, D.184, N.185 Ligands: H6N.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.158, B:D.184, H2O.9

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

SAH.2: 20 residues within 4Å: Chain A: A.56, L.57, V.58, E.80, G.82, V.83, Y.84, Y.87, S.88, D.106, V.107, N.108, Y.111, S.133, E.134, A.135, D.158, A.159, D.160, Y.167 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.84 Hydrogen bonds: A:A.56, A:V.58, A:G.82, A:Y.84, A:Y.87, A:S.88, A:S.88, A:V.107, A:E.134, A:A.135, A:D.158, A:D.160, A:Y.167 Water bridges: A:G.86, A:G.86, A:L.89, A:N.163, A:N.163 SAH.7: 21 residues within 4Å: Chain B: A.56, L.57, V.58, E.80, G.82, V.83, Y.84, Y.87, S.88, I.105, D.106, V.107, Y.111, S.133, E.134, A.135, D.158, A.159, D.160, Y.167 Ligands: H6N.8 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.84 Hydrogen bonds: B:A.56, B:V.58, B:G.82, B:Y.84, B:Y.87, B:S.88, B:S.88, B:V.107, B:A.135, B:D.160, B:D.160, B:Y.167 Water bridges: B:G.86, B:G.86, B:L.89, B:N.163, B:N.163

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: A.219, A.220, D.221, P.222 Chain B: P.35, R.36 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:A.219, B:R.36 GOL.4: 5 residues within 4Å: Chain A: P.35, R.36 Chain B: A.219, A.220, P.222 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.220, A:P.35

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 7 residues within 4Å: Chain B: K.16, E.49, S.54, T.55, L.57, V.58, A.59 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.16, B:E.49, B:L.57, B:V.58 Water bridges: B:A.60, B:A.60

1 x H6N: Protocatechuic aldehyde(Non-covalent)

H6N.8: 9 residues within 4Å: Chain B: K.16, T.55, A.56, D.158, K.161, D.184, N.185 Ligands: MG.6, SAH.7 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.56 Hydrogen bonds: B:K.16, B:D.158, B:K.161, B:N.185, B:N.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hnin, S.Y.Y. et al., Structure-Based Catalytic Mechanism of Amaryllidaceae O-Methyltransferases. Acs Catalysis (2024)

Release Date

2024-08-07

Peptides

O-methyltransferase family protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

O-methyltransferase family protein

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