SMTL ID : 7was.1

SbSOMT in complex with pterostilbene and nicotinamide adenine dinucleotide(NAD+)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x 3RL: Pterostilbene(Non-covalent)

3RL.1: 14 residues within 4Å: Chain A: M.142, I.143, F.188, M.192, W.278, H.281, D.282, Y.310, E.327, L.328, T.331, M.332, T.335 Chain B: L.27 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.143, A:I.143, A:F.188, A:W.278, A:L.328, A:T.331 Hydrogen bonds: A:E.327 3RL.10: 15 residues within 4Å: Chain A: L.27 Chain B: L.139, M.142, I.143, M.174, F.188, M.192, W.278, H.281, D.282, Y.310, L.328, M.332, T.335 Ligands: GOL.15 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.139, B:L.139, B:I.143, B:I.143, B:W.278, B:L.328

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 11 residues within 4Å: Chain A: G.220, Y.242, D.243, L.244, G.262, S.263, M.264, F.265, W.283, A.287, K.290 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.242, A:D.243, A:S.263, A:M.264, A:D.266 NAD.11: 13 residues within 4Å: Chain B: V.219, G.220, Y.242, D.243, L.244, G.262, S.263, M.264, F.265, W.283, D.284, A.287, K.290 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.287, B:K.290 Hydrogen bonds: B:Y.242, B:S.263, B:M.264, B:D.284, B:A.287 Water bridges: B:S.338

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: G.32, V.35, H.92 Chain B: K.28, G.32 Ligands: GOL.9 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.28, A:K.28, B:K.28 Water bridges: A:G.31, A:A.34 GOL.4: 6 residues within 4Å: Chain A: A.90, S.93, V.95, R.96, C.97 Chain B: P.316 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.93, A:R.96, A:C.97, A:C.97, B:P.316 GOL.9: 7 residues within 4Å: Chain A: K.28, G.32 Chain B: K.28, G.32, V.35, H.92 Ligands: GOL.3 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.32, B:K.28 Water bridges: B:A.34 GOL.12: 6 residues within 4Å: Chain A: P.316 Chain B: A.90, S.93, V.95, R.96, C.97 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.93, B:R.96, B:C.97, A:P.316 GOL.15: 7 residues within 4Å: Chain A: L.27, K.28, G.31 Chain B: Y.310, G.324, E.327 Ligands: 3RL.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.310, B:Y.310 GOL.16: 2 residues within 4Å: Chain B: A.249, P.253 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.249 GOL.17: 5 residues within 4Å: Chain B: E.167, G.171, M.172, P.173, E.176 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.171 GOL.18: 1 residues within 4Å: Chain B: N.236 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.236

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 8 residues within 4Å: Chain A: S.93, R.96, S.121, P.122, V.123 Chain B: S.22, F.25 Ligands: EDO.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.93, A:S.93, A:R.96, A:R.96, A:V.123

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 4 residues within 4Å: Chain A: R.16, N.17, D.20 Chain B: Y.364 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.16, A:D.20, A:D.20 Water bridges: A:R.16

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 3 residues within 4Å: Chain A: L.244, P.245, H.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.246, A:H.246 EDO.8: 2 residues within 4Å: Chain A: E.176, S.179 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.176, A:S.179, A:S.179 EDO.13: 6 residues within 4Å: Chain A: P.122, K.125 Chain B: E.18, E.19, S.22 Ligands: PG4.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.22, B:S.22 EDO.14: 3 residues within 4Å: Chain A: F.25 Chain B: S.93, R.96 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.96 EDO.19: 3 residues within 4Å: Chain B: R.238, V.257, E.258 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lui, A.C.W. et al., Regioselective stilbene O-methylations in Saccharinae grasses. Nat Commun (2023)

Release Date

2022-12-21

Peptides

stilbene O-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

stilbene O-methyltransferase

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