SMTL ID : 5x1k.1 (1 other biounit)

Vanillate/3-O-methylgallate O-demethylase, LigM, 3-O-methylgallate complex form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x 7WR: 3-methoxy-4,5-bis(oxidanyl)benzoic acid(Non-covalent)

7WR.1: 12 residues within 4Å: Chain A: Y.34, Q.60, H.63, M.64, R.125, Y.250, P.251, N.253, T.254, W.259, P.261, F.396 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.34, A:P.261, A:P.261 Hydrogen bonds: A:Y.250, A:P.251, A:N.253, A:T.254 Water bridges: A:Y.32 Salt bridges: A:R.125 pi-Stacking: A:W.259 7WR.7: 12 residues within 4Å: Chain B: Y.34, Q.60, H.63, M.64, R.125, Y.250, P.251, N.253, T.254, W.259, P.261, F.396 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.34, B:P.261, B:P.261 Hydrogen bonds: B:Y.250, B:P.251, B:N.253, B:T.254 Water bridges: B:Y.32 Salt bridges: B:R.125 pi-Stacking: B:W.259

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

TRS.2: 8 residues within 4Å: Chain A: G.431, G.432, T.433, R.434, K.435, V.438, E.439, P.440 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.431, A:K.435 TRS.8: 8 residues within 4Å: Chain B: G.431, G.432, T.433, R.434, K.435, V.438, E.439, P.440 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.431, B:K.435

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

PEG.3: 4 residues within 4Å: Chain A: K.228, N.231, A.232, E.235 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.232, A:E.235, A:E.235 PEG.9: 4 residues within 4Å: Chain B: K.228, N.231, A.232, E.235 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.232, B:E.235, B:E.235

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

EDO.4: 8 residues within 4Å: Chain A: G.292, G.293, N.374, Y.375, A.376, N.379, D.381, W.426 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.375, A:A.376, A:A.380, A:D.381 EDO.5: 4 residues within 4Å: Chain A: D.148, Q.161, R.162, I.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.162 EDO.6: 8 residues within 4Å: Chain A: L.264, Y.268, Y.285, E.286, G.289, A.290, N.377, T.378 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.285, A:G.289, A:A.290, A:A.290, A:T.378 EDO.10: 8 residues within 4Å: Chain B: G.292, G.293, N.374, Y.375, A.376, N.379, D.381, W.426 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.375, B:A.376, B:A.380, B:D.381 EDO.11: 4 residues within 4Å: Chain B: D.148, Q.161, R.162, I.163 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.162 EDO.12: 8 residues within 4Å: Chain B: L.264, Y.268, Y.285, E.286, G.289, A.290, N.377, T.378 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.285, B:G.289, B:A.290, B:A.290, B:T.378

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harada, A. et al., The crystal structure of a new O-demethylase from Sphingobium sp. strain SYK-6. FEBS J. (2017)

Release Date

2017-05-17

Peptides

Vanillate/3-O-methylgallate O-demethylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Vanillate/3-O-methylgallate O-demethylase

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