SMTL ID : 7w2j.1

Cryo-EM Structure of Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 36 residues within 4Å: Chain A: I.13, G.14, A.15, G.16, I.17, L.36, D.37, A.38, Y.64, A.74, Y.85, I.101, K.102, G.103, G.106, T.107, T.108, H.110, W.111, S.114, A.252, V.253, V.254, A.289, N.290, E.293, K.296, L.297, I.431, N.477, H.478, N.521, S.522, T.523, L.524, M.526 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Y.64, A:W.111, A:N.477 Hydrogen bonds: A:I.13, A:I.17, A:D.37, A:A.38, A:Y.85, A:Y.85, A:G.103, A:T.107, A:T.107, A:T.107, A:T.108, A:S.114, A:A.252, A:V.254, A:N.290, A:K.296, A:N.521, A:S.522, A:T.523, A:L.524 FAD.6: 36 residues within 4Å: Chain D: I.13, G.14, A.15, G.16, I.17, L.36, D.37, A.38, Y.64, A.74, Y.85, I.101, K.102, G.103, G.106, T.107, T.108, H.110, W.111, S.114, A.252, V.253, V.254, A.289, N.290, E.293, K.296, L.297, I.431, N.477, H.478, N.521, S.522, T.523, L.524, M.526 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:Y.64, D:W.111, D:N.477 Hydrogen bonds: D:I.13, D:I.17, D:D.37, D:A.38, D:Y.85, D:Y.85, D:G.103, D:T.107, D:T.107, D:T.107, D:T.108, D:S.114, D:A.252, D:V.254, D:N.290, D:K.296, D:N.521, D:S.522, D:T.523, D:L.524

2 x F3S: FE3-S4 CLUSTER(Covalent)

F3S.2: 14 residues within 4Å: Chain A: R.205, C.216, G.218, N.219, N.220, N.221, C.222, C.226, P.227, I.228, A.230, M.231, G.342, S.343 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.216, A:C.222, A:C.226 F3S.7: 14 residues within 4Å: Chain D: R.205, C.216, G.218, N.219, N.220, N.221, C.222, C.226, P.227, I.228, A.230, M.231, G.342, S.343 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.216, D:C.222, D:C.226

6 x HEC: HEME C(Covalent)

HEC.3: 23 residues within 4Å: Chain A: P.214, I.228 Chain C: A.261, R.262, V.342, C.343, C.346, H.347, Y.358, Y.359, P.360, L.362, N.365, T.367, S.379, I.380, V.384, R.386, I.393, L.394, M.395, P.396, F.398 21 PLIP interactions: 19 interactions with chain C, 2 interactions with chain A, Hydrophobic interactions: C:V.342, C:Y.358, C:Y.359, C:P.360, C:L.362, C:I.380, C:I.380, C:V.384, C:I.393, C:P.396, C:F.398, C:F.398, A:P.214, A:I.228 Hydrogen bonds: C:R.262, C:N.365, C:T.367, C:S.379, C:S.379 Salt bridges: C:R.262, C:R.386 HEC.4: 20 residues within 4Å: Chain C: A.199, H.200, C.201, C.204, H.205, W.228, R.229, A.230, P.231, I.233, W.244, Y.252, L.253, P.266, M.267, L.275, I.286, T.366, T.367, D.375 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:A.199, C:A.230, C:P.231, C:I.233, C:W.244, C:Y.252, C:L.253, C:L.275, C:I.286 Hydrogen bonds: C:T.366 Metal complexes: C:H.205 HEC.5: 21 residues within 4Å: Chain C: A.50, D.51, C.52, C.55, H.56, I.78, S.80, T.81, N.82, I.83, I.91, Y.94, F.99, A.102, L.114, Y.115, A.117, M.118, P.119, Y.123, R.161 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:A.50, C:I.78, C:I.83, C:I.91, C:F.99, C:F.99, C:A.102, C:L.114, C:Y.115, C:A.117, C:P.119 Hydrogen bonds: C:T.81 Salt bridges: C:R.161 Metal complexes: C:H.56 HEC.8: 23 residues within 4Å: Chain D: P.214, I.228 Chain F: A.261, R.262, V.342, C.343, C.346, H.347, Y.358, Y.359, P.360, L.362, N.365, T.367, S.379, I.380, V.384, R.386, I.393, L.394, M.395, P.396, F.398 21 PLIP interactions: 2 interactions with chain D, 19 interactions with chain F, Hydrophobic interactions: D:P.214, D:I.228, F:V.342, F:Y.358, F:Y.359, F:P.360, F:L.362, F:I.380, F:I.380, F:V.384, F:I.393, F:P.396, F:F.398, F:F.398 Hydrogen bonds: F:R.262, F:N.365, F:T.367, F:S.379, F:S.379 Salt bridges: F:R.262, F:R.386 HEC.9: 20 residues within 4Å: Chain F: A.199, H.200, C.201, C.204, H.205, W.228, R.229, A.230, P.231, I.233, W.244, Y.252, L.253, P.266, M.267, L.275, I.286, T.366, T.367, D.375 11 PLIP interactions: 11 interactions with chain F, Hydrophobic interactions: F:A.199, F:A.230, F:P.231, F:I.233, F:W.244, F:Y.252, F:L.253, F:L.275, F:I.286 Hydrogen bonds: F:T.366 Metal complexes: F:H.205 HEC.10: 21 residues within 4Å: Chain F: A.50, D.51, C.52, C.55, H.56, I.78, S.80, T.81, N.82, I.83, I.91, Y.94, F.99, A.102, L.114, Y.115, A.117, M.118, P.119, Y.123, R.161 14 PLIP interactions: 14 interactions with chain F, Hydrophobic interactions: F:A.50, F:I.78, F:I.83, F:I.91, F:F.99, F:F.99, F:A.102, F:L.114, F:Y.115, F:A.117, F:P.119 Hydrogen bonds: F:T.81 Salt bridges: F:R.161 Metal complexes: F:H.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, Y. et al., Essential Insight of Direct Electron Transfer-Type Bioelectrocatalysis by Membrane-Bound d-Fructose Dehydrogenase with Structural Bioelectrochemistry. Acs Catalysis (2023)

Release Date

2022-11-30

Peptides

Fructose dehydrogenase large subunit: AD
Fructose dehydrogenase small subunit: BE
Fructose dehydrogenase cytochrome subunit: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Fructose dehydrogenase large subunit

Fructose dehydrogenase small subunit

Fructose dehydrogenase cytochrome subunit

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