SMTL ID : 8ot8.1

Alditol oxidase from Actinomycetota bacterium in complex with D-xylulose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 35 residues within 4Å: Chain A: W.8, R.39, V.40, L.41, G.42, S.43, G.44, H.45, S.46, F.47, I.50, T.51, A.80, A.102, S.103, L.104, C.108, A.110, G.111, A.112, A.114, T.115, T.117, H.118, L.162, G.163, G.166, A.167, V.168, Q.295, R.329, H.379, G.381, K.382 Ligands: XUL.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:W.8, A:W.8, A:H.45, A:F.47, A:L.104 Hydrogen bonds: A:V.40, A:G.42, A:S.43, A:S.43, A:G.44, A:H.45, A:I.50, A:T.51, A:S.103, A:T.117, A:T.117, A:H.118, A:H.118, A:V.168, A:V.168, A:R.329, A:R.329, A:G.381, A:K.382 pi-Cation interactions: A:K.382 FAD.3: 38 residues within 4Å: Chain B: W.8, R.39, V.40, L.41, G.42, S.43, G.44, H.45, S.46, F.47, I.50, T.51, L.60, A.80, A.102, S.103, L.104, I.107, C.108, A.110, G.111, A.112, A.114, T.115, T.117, H.118, L.162, G.163, G.166, A.167, V.168, Q.295, E.297, R.329, H.379, G.381, K.382 Ligands: XUL.4 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:W.8, B:W.8, B:H.45, B:F.47, B:L.104, B:I.107 Hydrogen bonds: B:V.40, B:V.40, B:G.42, B:S.43, B:G.44, B:H.45, B:S.46, B:T.51, B:T.51, B:S.103, B:C.108, B:T.115, B:T.115, B:T.117, B:H.118, B:H.118, B:V.168, B:V.168, B:R.329, B:R.329, B:G.381, B:K.382 pi-Stacking: B:H.118 FAD.5: 37 residues within 4Å: Chain C: W.8, R.39, V.40, L.41, G.42, S.43, G.44, H.45, S.46, F.47, I.50, T.51, L.60, A.80, A.102, S.103, L.104, I.107, C.108, A.110, G.111, A.112, A.114, T.115, T.117, H.118, L.162, G.163, G.166, A.167, V.168, Q.295, R.329, H.379, G.381, K.382 Ligands: XUL.6 28 PLIP interactions: 28 interactions with chain C Hydrophobic interactions: C:W.8, C:W.8, C:H.45, C:F.47, C:F.47, C:L.104 Hydrogen bonds: C:R.39, C:V.40, C:G.42, C:S.43, C:S.43, C:G.44, C:H.45, C:S.46, C:T.51, C:S.103, C:C.108, C:T.115, C:T.117, C:H.118, C:H.118, C:V.168, C:V.168, C:R.329, C:R.329, C:G.381, C:K.382 pi-Cation interactions: C:K.382 FAD.7: 37 residues within 4Å: Chain D: W.8, R.39, V.40, L.41, G.42, S.43, G.44, H.45, S.46, F.47, I.50, T.51, A.80, A.102, S.103, L.104, I.107, C.108, A.110, G.111, A.112, A.114, T.115, T.117, H.118, L.162, G.163, G.166, A.167, V.168, Q.295, E.297, R.329, H.379, G.381, K.382 Ligands: XUL.8 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:W.8, D:H.45, D:F.47, D:L.104 Hydrogen bonds: D:V.40, D:G.42, D:S.43, D:S.43, D:H.45, D:S.46, D:T.51, D:T.51, D:S.103, D:C.108, D:T.115, D:T.117, D:T.117, D:H.118, D:H.118, D:V.168, D:V.168, D:R.329, D:R.329, D:G.381, D:K.382 pi-Stacking: D:H.118

4 x XUL: D-XYLULOSE(Non-covalent)

XUL.2: 11 residues within 4Å: Chain A: S.103, F.211, H.281, F.282, Q.295, E.327, R.329, H.350, T.352, K.382 Ligands: FAD.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.103, A:S.103, A:Q.295, A:E.327, A:E.327, A:R.329, A:R.329, A:T.352, A:K.382 XUL.4: 10 residues within 4Å: Chain B: S.103, F.282, Q.295, I.325, E.327, R.329, H.350, T.352, K.382 Ligands: FAD.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.103, B:Q.295, B:T.352, B:T.352, B:K.382, B:K.382 XUL.6: 12 residues within 4Å: Chain C: S.103, P.256, V.257, F.282, Q.295, I.325, E.327, R.329, H.350, T.352, K.382 Ligands: FAD.5 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:S.103, C:Q.295, C:E.327, C:E.327, C:R.329, C:H.350, C:T.352, C:K.382, C:K.382 XUL.8: 10 residues within 4Å: Chain D: S.103, F.282, Q.295, I.325, E.327, R.329, H.350, T.352, K.382 Ligands: FAD.7 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.103, D:S.103, D:R.329, D:R.329, D:H.350, D:T.352, D:K.382, D:K.382

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Santema, L.L. et al., Discovery and biochemical characterization of thermostable glycerol oxidases. Appl.Microbiol.Biotechnol. (2024)

Release Date

2024-02-28

Peptides

FAD-binding protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

FAD-binding protein