SMTL ID : 7ywu.1 (3 other biounits)

Eugenol oxidase from rhodococcus jostii: mutant S81H, A423M, H434Y, S394V, I445D, S518P

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 29 residues within 4Å: Chain A: H.81, P.82, V.83, S.84, T.85, G.86, K.87, N.88, N.89, T.106, P.150, D.151, L.152, G.155, S.156, G.159, N.160, L.162, G.165, V.166, Y.168, G.225, I.226, V.227, L.381, H.390, R.472, K.513 Ligands: EOL.5 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:L.152, A:L.381 Hydrogen bonds: A:S.84, A:T.85, A:T.85, A:G.86, A:K.87, A:N.88, A:N.88, A:T.106, A:D.151, A:S.156, A:N.160, A:V.166, A:V.166, A:V.227, A:V.227, A:R.472, A:R.472, A:K.513 FAD.6: 31 residues within 4Å: Chain B: Y.44, H.81, P.82, V.83, S.84, T.85, G.86, K.87, N.88, N.89, T.106, P.150, D.151, L.152, G.155, S.156, G.159, N.160, L.162, D.163, G.165, V.166, Y.168, G.225, I.226, V.227, H.390, L.438, R.472, K.513 Ligands: EOL.8 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:Y.44, B:L.152, B:L.438 Hydrogen bonds: B:S.84, B:T.85, B:G.86, B:K.87, B:N.88, B:N.88, B:N.89, B:N.89, B:D.151, B:S.156, B:N.160, B:V.166, B:V.166, B:Y.168, B:V.227, B:V.227, B:R.472, B:R.472, B:K.513

3 x HEZ: HEXANE-1,6-DIOL(Non-covalent)

HEZ.2: 6 residues within 4Å: Chain A: N.267 Chain B: P.170, Y.171, W.177, M.235, M.268 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.267, B:P.170 Hydrophobic interactions: B:Y.171 HEZ.3: 8 residues within 4Å: Chain A: R.290, D.297, G.298, V.385, N.419, K.420, D.421, I.440 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.385 Hydrogen bonds: A:D.297, A:D.297, A:D.421, A:D.421, A:I.440 HEZ.7: 8 residues within 4Å: Chain A: M.176, P.208, Y.209 Chain B: F.175, M.176, Q.178, P.208, F.214 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.209 Hydrogen bonds: B:Q.178

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: V.166, G.172, D.173, V.274, G.429, E.432, Y.434 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.172, A:E.432

2 x EOL: 2-methoxy-4-(prop-2-en-1-yl)phenol(Non-covalent)

EOL.5: 12 residues within 4Å: Chain A: Y.91, D.151, Y.168, E.378, G.392, Q.425, I.427, V.436, L.438, Y.471, R.472 Ligands: FAD.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.427, A:V.436 Hydrogen bonds: A:Y.91, A:Y.471, A:R.472 EOL.8: 15 residues within 4Å: Chain B: Y.91, D.151, Y.168, R.278, M.282, E.378, H.390, G.392, Q.425, I.427, V.436, L.438, Y.471, R.472 Ligands: FAD.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.427, B:V.436, B:V.436 Hydrogen bonds: B:Y.91, B:Y.91, B:R.472

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, Y. et al., Structure- and computational-aided engineering of an oxidase to produce isoeugenol from a lignin-derived compound. Nat Commun (2022)

Release Date

2022-11-16

Peptides

Probable vanillyl-alcohol oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Probable vanillyl-alcohol oxidase

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