SMTL ID : 5mxu.1

Structure of the Y503F mutant of vanillyl alcohol oxidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-octamer

Ligands

8 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 31 residues within 4Å: Chain A: W.98, P.99, I.100, S.101, I.102, G.103, R.104, N.105, S.106, Y.108, G.110, P.169, D.170, L.171, G.174, S.175, L.177, N.179, E.182, G.184, V.185, Y.187, G.260, I.261, V.262, E.410, W.413, H.422, F.424, R.504, K.545 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:D.170, A:L.171, A:W.413 Hydrogen bonds: A:S.101, A:S.101, A:I.102, A:G.103, A:R.104, A:N.105, A:D.170, A:D.170, A:S.175, A:N.179, A:N.179, A:V.185, A:V.185, A:Y.187, A:V.262, A:R.504, A:R.504, A:K.545 Water bridges: A:L.171 pi-Stacking: A:F.424 FAD.2: 28 residues within 4Å: Chain B: W.98, P.99, I.100, S.101, I.102, G.103, R.104, N.105, S.106, P.169, D.170, L.171, G.174, S.175, N.179, E.182, G.184, V.185, Y.187, G.260, I.261, V.262, W.413, I.414, H.422, F.424, R.504, K.545 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:D.170, B:L.171, B:W.413, B:I.414 Hydrogen bonds: B:S.101, B:S.101, B:I.102, B:G.103, B:R.104, B:N.105, B:D.170, B:S.175, B:N.179, B:N.179, B:V.185, B:V.185, B:V.262, B:R.504, B:R.504, B:K.545 Water bridges: B:N.105, B:L.171 pi-Stacking: B:F.424 FAD.5: 31 residues within 4Å: Chain C: W.98, P.99, I.100, S.101, I.102, G.103, R.104, N.105, S.106, Y.108, G.110, P.169, D.170, L.171, G.174, S.175, L.177, N.179, E.182, G.184, V.185, Y.187, G.260, I.261, V.262, E.410, W.413, H.422, F.424, R.504, K.545 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:D.170, C:L.171, C:W.413 Hydrogen bonds: C:S.101, C:S.101, C:I.102, C:G.103, C:R.104, C:N.105, C:D.170, C:D.170, C:S.175, C:N.179, C:N.179, C:V.185, C:V.185, C:Y.187, C:V.262, C:R.504, C:R.504, C:K.545 Water bridges: C:L.171 pi-Stacking: C:F.424 FAD.6: 28 residues within 4Å: Chain D: W.98, P.99, I.100, S.101, I.102, G.103, R.104, N.105, S.106, P.169, D.170, L.171, G.174, S.175, N.179, E.182, G.184, V.185, Y.187, G.260, I.261, V.262, W.413, I.414, H.422, F.424, R.504, K.545 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:D.170, D:L.171, D:W.413, D:I.414 Hydrogen bonds: D:S.101, D:S.101, D:I.102, D:G.103, D:R.104, D:N.105, D:D.170, D:S.175, D:N.179, D:N.179, D:V.185, D:V.185, D:V.262, D:R.504, D:R.504, D:K.545 Water bridges: D:N.105, D:L.171 pi-Stacking: D:F.424 FAD.9: 31 residues within 4Å: Chain E: W.98, P.99, I.100, S.101, I.102, G.103, R.104, N.105, S.106, Y.108, G.110, P.169, D.170, L.171, G.174, S.175, L.177, N.179, E.182, G.184, V.185, Y.187, G.260, I.261, V.262, E.410, W.413, H.422, F.424, R.504, K.545 23 PLIP interactions: 23 interactions with chain E Hydrophobic interactions: E:D.170, E:L.171, E:W.413 Hydrogen bonds: E:S.101, E:S.101, E:I.102, E:G.103, E:R.104, E:N.105, E:D.170, E:D.170, E:S.175, E:N.179, E:N.179, E:V.185, E:V.185, E:Y.187, E:V.262, E:R.504, E:R.504, E:K.545 Water bridges: E:L.171 pi-Stacking: E:F.424 FAD.10: 28 residues within 4Å: Chain F: W.98, P.99, I.100, S.101, I.102, G.103, R.104, N.105, S.106, P.169, D.170, L.171, G.174, S.175, N.179, E.182, G.184, V.185, Y.187, G.260, I.261, V.262, W.413, I.414, H.422, F.424, R.504, K.545 23 PLIP interactions: 23 interactions with chain F Hydrophobic interactions: F:D.170, F:L.171, F:W.413, F:I.414 Hydrogen bonds: F:S.101, F:S.101, F:I.102, F:G.103, F:R.104, F:N.105, F:D.170, F:S.175, F:N.179, F:N.179, F:V.185, F:V.185, F:V.262, F:R.504, F:R.504, F:K.545 Water bridges: F:N.105, F:L.171 pi-Stacking: F:F.424 FAD.13: 31 residues within 4Å: Chain G: W.98, P.99, I.100, S.101, I.102, G.103, R.104, N.105, S.106, Y.108, G.110, P.169, D.170, L.171, G.174, S.175, L.177, N.179, E.182, G.184, V.185, Y.187, G.260, I.261, V.262, E.410, W.413, H.422, F.424, R.504, K.545 23 PLIP interactions: 23 interactions with chain G Hydrophobic interactions: G:D.170, G:L.171, G:W.413 Hydrogen bonds: G:S.101, G:S.101, G:I.102, G:G.103, G:R.104, G:N.105, G:D.170, G:D.170, G:S.175, G:N.179, G:N.179, G:V.185, G:V.185, G:Y.187, G:V.262, G:R.504, G:R.504, G:K.545 Water bridges: G:L.171 pi-Stacking: G:F.424 FAD.14: 28 residues within 4Å: Chain H: W.98, P.99, I.100, S.101, I.102, G.103, R.104, N.105, S.106, P.169, D.170, L.171, G.174, S.175, N.179, E.182, G.184, V.185, Y.187, G.260, I.261, V.262, W.413, I.414, H.422, F.424, R.504, K.545 23 PLIP interactions: 23 interactions with chain H Hydrophobic interactions: H:D.170, H:L.171, H:W.413, H:I.414 Hydrogen bonds: H:S.101, H:S.101, H:I.102, H:G.103, H:R.104, H:N.105, H:D.170, H:S.175, H:N.179, H:N.179, H:V.185, H:V.185, H:V.262, H:R.504, H:R.504, H:K.545 Water bridges: H:N.105, H:L.171 pi-Stacking: H:F.424

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain B: L.321, N.392, V.397, D.409, K.412 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.409, B:D.409, B:K.412 GOL.4: 2 residues within 4Å: Chain B: Q.512, L.560 No protein-ligand interaction detected (PLIP) GOL.7: 5 residues within 4Å: Chain D: L.321, N.392, V.397, D.409, K.412 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.409, D:D.409, D:K.412 GOL.8: 2 residues within 4Å: Chain D: Q.512, L.560 No protein-ligand interaction detected (PLIP) GOL.11: 5 residues within 4Å: Chain F: L.321, N.392, V.397, D.409, K.412 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.409, F:D.409, F:K.412 GOL.12: 2 residues within 4Å: Chain F: Q.512, L.560 No protein-ligand interaction detected (PLIP) GOL.15: 5 residues within 4Å: Chain H: L.321, N.392, V.397, D.409, K.412 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:D.409, H:D.409, H:K.412 GOL.16: 2 residues within 4Å: Chain H: Q.512, L.560 No protein-ligand interaction detected (PLIP)

Links

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Citation

Ewing, T.A. et al., Two tyrosine residues, Tyr-108 and Tyr-503, are responsible for the deprotonation of phenolic substrates in vanillyl-alcohol oxidase. J. Biol. Chem. (2017)

Release Date

2017-07-26

Peptides

Vanillyl-alcohol oxidase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Vanillyl-alcohol oxidase