SMTL ID : 7wh9.1

holo structure of emodin 1-OH O-methyltransferase complex with emodin and S-Adenosyl-L-homocysteine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-hexamer

Ligands

6 x EMO: 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE(Non-covalent)

EMO.1: 16 residues within 4Å: Chain A: Y.193, L.196, E.200, A.201, R.238, W.239, M.289, Y.390, H.393, D.394, R.454, T.457, M.458, A.461, I.462 Ligands: SAH.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.196, A:E.200, A:T.457, A:A.461 Hydrogen bonds: A:R.238, A:Y.390, A:R.454 EMO.3: 17 residues within 4Å: Chain B: Y.193, L.196, E.200, A.201, R.238, W.239, M.285, M.289, Y.390, H.393, D.394, R.454, T.457, M.458, A.461, I.462 Ligands: SAH.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.193, B:L.196, B:E.200, B:T.457 Hydrogen bonds: B:R.238, B:R.238, B:Y.390, B:R.454 EMO.5: 16 residues within 4Å: Chain C: Y.193, L.196, E.200, A.201, R.238, W.239, M.289, Y.390, H.393, D.394, R.454, T.457, M.458, A.461, I.462 Ligands: SAH.6 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Y.193, C:L.196, C:L.196, C:E.200, C:T.457, C:A.461 Hydrogen bonds: C:Y.193, C:R.238, C:Y.390, C:D.394, C:R.454 EMO.7: 16 residues within 4Å: Chain D: Y.193, L.196, E.200, A.201, R.238, W.239, M.289, Y.390, H.393, D.394, R.454, T.457, M.458, A.461, I.462 Ligands: SAH.8 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.196, D:E.200, D:T.457, D:A.461 Hydrogen bonds: D:Y.193, D:R.238, D:Y.390, D:R.454 EMO.9: 17 residues within 4Å: Chain E: Y.193, L.196, E.200, A.201, R.238, W.239, M.285, M.289, Y.390, H.393, D.394, R.454, T.457, M.458, A.461, I.462 Ligands: SAH.10 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:Y.193, E:L.196, E:E.200, E:T.457 Hydrogen bonds: E:Y.193, E:R.238, E:R.238, E:Y.390, E:R.454 EMO.11: 16 residues within 4Å: Chain F: Y.193, L.196, E.200, A.201, R.238, W.239, M.289, Y.390, H.393, D.394, R.454, T.457, M.458, A.461, I.462 Ligands: SAH.12 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:Y.193, F:L.196, F:L.196, F:E.200, F:T.457, F:A.461 Hydrogen bonds: F:R.238, F:Y.390, F:R.454

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

SAH.2: 16 residues within 4Å: Chain A: W.239, M.289, G.318, G.319, G.320, D.341, R.342, V.345, H.372, S.373, F.374, F.375, R.389, Y.390, D.394 Ligands: EMO.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.318, A:R.342, A:S.373, A:F.374, A:R.389 Water bridges: A:F.324, A:D.394 Salt bridges: A:R.389 pi-Stacking: A:W.239, A:W.239, A:F.374 SAH.4: 16 residues within 4Å: Chain B: W.239, M.289, G.318, G.319, G.320, D.341, R.342, H.372, S.373, F.374, F.375, R.389, Y.390, D.394, W.395 Ligands: EMO.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:M.289 Hydrogen bonds: B:G.318, B:R.342, B:S.373, B:F.374, B:R.389 Salt bridges: B:R.389 pi-Stacking: B:W.239, B:W.239, B:F.374 SAH.6: 17 residues within 4Å: Chain C: W.239, M.289, G.318, G.319, G.320, D.341, R.342, V.345, H.372, S.373, F.374, R.389, Y.390, V.391, D.394, W.395 Ligands: EMO.5 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.318, C:S.373, C:F.374, C:R.389 Salt bridges: C:R.389 pi-Stacking: C:W.239, C:W.239, C:F.374 SAH.8: 16 residues within 4Å: Chain D: W.239, M.289, G.318, G.319, G.320, D.341, R.342, V.345, H.372, S.373, F.374, F.375, R.389, Y.390, D.394 Ligands: EMO.7 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.318, D:R.342, D:S.373, D:F.374, D:R.389 Water bridges: D:F.324 Salt bridges: D:R.389 pi-Stacking: D:W.239, D:W.239, D:F.374 SAH.10: 16 residues within 4Å: Chain E: W.239, M.289, G.318, G.319, G.320, D.341, R.342, H.372, S.373, F.374, F.375, R.389, Y.390, D.394, W.395 Ligands: EMO.9 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:M.289 Hydrogen bonds: E:G.318, E:D.341, E:R.342, E:S.373, E:F.374, E:R.389 Salt bridges: E:R.389 pi-Stacking: E:W.239, E:W.239, E:F.374 SAH.12: 17 residues within 4Å: Chain F: W.239, M.289, G.318, G.319, G.320, D.341, R.342, V.345, H.372, S.373, F.374, R.389, Y.390, V.391, D.394, W.395 Ligands: EMO.11 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:G.318, F:S.373, F:F.374, F:R.389 Salt bridges: F:R.389 pi-Stacking: F:W.239, F:W.239, F:F.374

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xue, Y. et al., Characterization and Structural Analysis of Emodin- O -Methyltransferase from Aspergillus terreus. J.Agric.Food Chem. (2022)

Release Date

2023-01-11

Peptides

O-methyltransferase gedA: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

O-methyltransferase gedA