SMTL ID : 8xdq.1

O-methyltransferase from Lycoris aurea complexed with Mg and SAH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

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

TRS.1: 4 residues within 4Å: Chain A: I.14, H.15, K.16, N.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.14, A:K.16, A:N.17 Water bridges: A:N.17

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: F.194, E.196, Y.197, P.198 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.196 GOL.5: 6 residues within 4Å: Chain A: A.219, A.220, D.221, P.222 Chain B: P.35, R.36 1 PLIP interactions: 1 interactions with chain B Water bridges: B:P.35 GOL.6: 6 residues within 4Å: Chain A: P.35, R.36 Chain B: A.219, A.220, D.221, P.222 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:A.220, A:P.35

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 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.5, H2O.6 MG.7: 4 residues within 4Å: Chain B: D.158, K.161, D.184, N.185 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.158, B:D.184, H2O.9, H2O.12, H2O.13

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

SAH.4: 18 residues within 4Å: Chain A: A.56, L.57, V.58, G.82, V.83, Y.84, Y.87, S.88, D.106, V.107, Y.111, S.133, E.134, A.135, D.158, A.159, D.160, Y.167 18 PLIP interactions: 18 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: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.8: 18 residues within 4Å: Chain B: A.56, L.57, V.58, G.82, V.83, Y.84, Y.87, S.88, D.106, V.107, Y.111, S.133, E.134, A.135, D.158, A.159, D.160, Y.167 17 PLIP interactions: 17 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 Water bridges: B:G.86, B:G.86, B:L.89, B:N.163, B:N.163

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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