SMTL ID : 7vb8.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

2 x STL: RESVERATROL(Non-covalent)

STL.1: 13 residues within 4Å: Chain A: M.143, I.144, M.175, F.189, M.193, W.279, H.282, D.283, Y.311, L.329, M.333, T.336 Chain B: L.28 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.144, A:I.144, A:F.189, A:L.329 Hydrogen bonds: A:D.283 Water bridges: A:E.328, A:E.328, A:T.336, B:L.28 pi-Stacking: A:W.279 STL.12: 13 residues within 4Å: Chain A: L.28 Chain B: M.143, I.144, M.175, F.189, M.193, W.279, H.282, D.283, Y.311, L.329, M.333, T.336 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.144, B:I.144, B:F.189, B:L.329 Hydrogen bonds: B:D.283 Water bridges: B:E.328, B:E.328, B:E.328 pi-Stacking: B:W.279

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

NAD.2: 15 residues within 4Å: Chain A: F.176, V.220, G.221, Y.243, D.244, L.245, G.263, S.264, M.265, F.266, W.284, D.285, K.287, A.288, K.291 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:K.287, A:A.288 Hydrogen bonds: A:G.221, A:Y.243, A:M.265, A:K.291 Water bridges: A:F.176, A:S.339, A:S.339, A:S.339 NAD.13: 15 residues within 4Å: Chain B: F.176, V.220, G.221, Y.243, D.244, L.245, G.263, S.264, M.265, F.266, D.267, W.284, A.288, K.291 Ligands: GOL.17 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.266, B:F.266, B:F.266, B:W.284 Hydrogen bonds: B:G.221, B:Y.243, B:S.264, B:M.265, B:D.267 Water bridges: B:A.288, B:A.288

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

EDO.3: 6 residues within 4Å: Chain A: E.45, L.46, A.68, V.69 Chain B: T.157, L.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.68 Water bridges: A:R.130 EDO.4: 5 residues within 4Å: Chain A: N.268, I.269, R.271, T.298, A.299 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.268, A:T.298, A:T.298 Water bridges: A:I.269, A:R.271 EDO.5: 3 residues within 4Å: Chain A: E.63, A.66, A.67 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.66 EDO.6: 6 residues within 4Å: Chain A: K.305, E.360, K.362, E.374, F.375, T.376 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.360, A:K.362, A:E.374 Water bridges: A:T.376 EDO.14: 5 residues within 4Å: Chain A: G.33 Chain B: K.29, G.33, V.36, H.93 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.29 Water bridges: B:K.29, B:A.35, A:E.328 EDO.15: 1 residues within 4Å: Chain B: P.184 No protein-ligand interaction detected (PLIP) EDO.16: 3 residues within 4Å: Chain B: S.180, N.186, H.247 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.186, B:H.247 EDO.18: 5 residues within 4Å: Chain B: I.44, E.45, R.130, L.138, M.142 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.130, B:R.130 EDO.24: 2 residues within 4Å: Chain B: D.285, K.287 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.285 EDO.25: 3 residues within 4Å: Chain B: F.176, W.284, F.337 2 PLIP interactions: 2 interactions with chain B Water bridges: B:F.337, B:S.339 EDO.26: 5 residues within 4Å: Chain A: P.123, K.126 Chain B: E.19, E.20, S.23 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.20 Water bridges: B:E.19, B:S.23

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 6 residues within 4Å: Chain A: K.41, I.44, E.45, G.141, M.142, L.145 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.145 Water bridges: A:K.41 Salt bridges: A:K.41 ACT.8: 4 residues within 4Å: Chain A: H.93 Chain B: F.26, Q.324 Ligands: GOL.28 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.324 Salt bridges: A:H.93 ACT.19: 5 residues within 4Å: Chain B: K.41, I.44, E.45, G.141, M.142 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.45 Salt bridges: B:K.41

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 2 residues within 4Å: Chain A: V.258, E.259 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.239, A:V.258 GOL.17: 4 residues within 4Å: Chain B: F.176, H.190, D.244 Ligands: NAD.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.190 GOL.20: 7 residues within 4Å: Chain A: P.317 Chain B: A.91, S.94, V.96, R.97, C.98 Ligands: GOL.22 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:C.98, B:C.98, A:P.317 GOL.21: 5 residues within 4Å: Chain B: E.62, E.77, D.107, D.108, A.109 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.107, B:D.108, B:A.109 GOL.22: 5 residues within 4Å: Chain B: S.94, R.97, S.122, P.123 Ligands: GOL.20 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.97, B:S.122, B:S.122 GOL.23: 4 residues within 4Å: Chain B: D.158, L.161, E.162, K.169 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.162, B:K.169 GOL.27: 3 residues within 4Å: Chain B: N.146, K.147, T.148 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.146, B:N.146, B:T.148, B:T.148 Water bridges: B:K.147 GOL.28: 5 residues within 4Å: Chain A: K.29 Chain B: P.319, L.321, Q.324 Ligands: ACT.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.321, B:Q.324, B:Q.324

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 4 residues within 4Å: Chain A: R.75, P.76, E.77, V.78 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: P.246, H.247 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain B: R.75, P.76, E.77, V.78 Ligand excluded by PLIP

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

2022-09-07

Peptides

stilbene O-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

stilbene O-methyltransferase