SMTL ID : 7war.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x 8KZ: 3-[(E)-2-(4-hydroxyphenyl)ethenyl]-5-methoxy-phenol(Non-covalent)

8KZ.1: 14 residues within 4Å: Chain A: M.142, I.143, M.174, F.188, M.192, W.278, H.281, D.282, Y.310, L.328, M.332, T.335 Chain B: L.27 Ligands: ACT.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.143, A:I.143, A:F.188, A:L.328 Hydrogen bonds: A:W.278 Water bridges: A:E.327, A:E.327 pi-Stacking: A:W.278 8KZ.20: 17 residues within 4Å: Chain A: L.27 Chain B: M.142, I.143, M.174, F.188, M.192, W.278, H.281, D.282, Y.310, E.327, L.328, T.331, M.332, T.335 Ligands: GOL.26, ACT.29 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.143, B:I.143, B:F.188, B:L.328, B:T.331 Hydrogen bonds: B:W.278 Water bridges: B:E.327, A:L.27 pi-Stacking: B:W.278

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

NAD.2: 16 residues within 4Å: Chain A: F.175, G.220, Y.242, D.243, L.244, G.262, S.263, M.264, F.265, W.283, D.284, A.287, K.290, S.338 Ligands: GOL.3, GOL.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.287 Hydrogen bonds: A:G.220, A:Y.242, A:M.264, A:D.284, A:D.284, A:K.290, A:S.338 NAD.21: 14 residues within 4Å: Chain B: F.175, V.219, G.220, Y.242, D.243, L.244, G.262, S.263, M.264, F.265, D.266, W.283, A.287 Ligands: EDO.28 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.265, B:F.265, B:W.283 Hydrogen bonds: B:G.220, B:Y.242, B:S.263, B:M.264, B:D.266 Water bridges: B:D.282, B:A.287

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: F.188, H.189, G.220, D.243 Ligands: NAD.2, ACT.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.189, A:G.220 GOL.5: 6 residues within 4Å: Chain A: F.175, D.282, W.283, F.336 Ligands: NAD.2, EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.283 Water bridges: A:D.284, A:G.339 GOL.7: 5 residues within 4Å: Chain A: D.150, Q.153, N.154, T.169 Chain B: K.146 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.150, A:D.150, A:N.154, B:K.146 GOL.10: 6 residues within 4Å: Chain A: A.90, S.93, V.95, R.96, C.97 Chain B: P.316 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.95, A:C.97, B:P.316 GOL.11: 4 residues within 4Å: Chain A: N.185, H.189, H.246, Q.250 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.189, A:Q.250 GOL.12: 5 residues within 4Å: Chain A: G.209, K.304, K.361, E.373, T.375 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.304, A:K.304, A:T.375, A:T.375 Water bridges: A:K.361 GOL.14: 4 residues within 4Å: Chain A: F.206, T.363, Y.364 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.364, A:Y.364 GOL.15: 6 residues within 4Å: Chain A: K.28, H.92 Chain B: K.28, L.29 Ligands: EDO.16, 1PE.19 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.28, A:K.28, A:H.92, B:K.28 GOL.18: 7 residues within 4Å: Chain A: F.37, L.149, D.150, Q.153 Chain B: L.149, D.150, Q.153 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.149, A:Q.153, B:K.146 GOL.23: 5 residues within 4Å: Chain B: F.175, D.282, W.283, F.336 Ligands: EDO.28 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.282, B:F.336 Water bridges: B:G.339 GOL.25: 6 residues within 4Å: Chain A: P.316 Chain B: A.90, S.93, V.95, R.96, C.97 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:P.316, B:R.96, B:C.97, B:C.97 GOL.26: 7 residues within 4Å: Chain A: F.33 Chain B: M.142, I.143, F.148, L.149, W.152 Ligands: 8KZ.20 1 PLIP interactions: 1 interactions with chain B Water bridges: B:F.148 GOL.27: 7 residues within 4Å: Chain A: D.285, K.340 Chain B: T.80, D.107, T.109, T.110, T.111 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.111, A:K.340 Water bridges: B:T.80, B:T.80, A:D.285, A:D.285 GOL.30: 7 residues within 4Å: Chain B: Y.310, V.311, P.313, A.321, A.325, N.368, W.370 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.311, B:W.370 Water bridges: B:T.319

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

EDO.4: 6 residues within 4Å: Chain A: F.206, Y.364, I.365 Chain B: R.16 Ligands: GOL.14, EDO.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.364 EDO.6: 4 residues within 4Å: Chain A: L.320, Q.323 Chain B: K.28 Ligands: 1PE.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.323 EDO.8: 7 residues within 4Å: Chain A: G.162, A.163, A.164, F.336 Chain B: R.74, V.77 Ligands: GOL.5 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:A.164 Hydrogen bonds: B:R.74 EDO.16: 7 residues within 4Å: Chain A: K.28, G.32, V.35, H.92 Chain B: G.32 Ligands: GOL.15, 1PE.19 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.28, A:A.34, A:H.92 EDO.17: 6 residues within 4Å: Chain A: K.202, K.205, F.206 Chain B: N.17, E.19 Ligands: EDO.4 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.202, A:K.205, B:N.17, B:N.17 EDO.22: 3 residues within 4Å: Chain A: V.123 Chain B: E.21, S.22 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:V.123 Hydrogen bonds: B:S.22 EDO.28: 3 residues within 4Å: Chain B: W.283 Ligands: NAD.21, GOL.23 No protein-ligand interaction detected (PLIP)

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

ACT.9: 6 residues within 4Å: Chain A: F.175, F.188, W.278, D.282 Ligands: 8KZ.1, GOL.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.175, A:F.188 ACT.29: 4 residues within 4Å: Chain B: M.192, W.278, D.282 Ligands: 8KZ.20 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.278

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

PEG.13: 5 residues within 4Å: Chain A: S.179, T.180, N.181, G.182, P.183 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.179, A:G.182 PEG.24: 8 residues within 4Å: Chain A: R.74, V.77 Chain B: G.162, A.163, A.164, E.167, F.336, S.338 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.74, B:A.164, B:E.167

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.19: 14 residues within 4Å: Chain A: K.28, L.29, G.32, Q.323, E.327 Chain B: K.28, G.31, G.32, V.35, P.36, H.92 Ligands: EDO.6, GOL.15, EDO.16 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.28, B:G.31, B:H.92, A:Q.323, A:E.327 Water bridges: B:A.34, B:A.34

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
B

B
A

stilbene O-methyltransferase

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