SMTL ID : 8k6k.1

Cryo-EM Structure of Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus variant-N1146A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

FAD.1: 35 residues within 4Å: Chain A: I.13, G.14, A.15, G.16, I.17, C.18, D.37, A.38, G.39, Y.64, G.99, K.102, G.103, G.106, T.107, T.108, H.110, W.111, A.112, A.113, S.114, M.223, A.252, V.253, V.254, A.288, A.289, N.290, E.293, A.477, H.478, N.521, S.522, T.523, M.526 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Y.64, A:T.107, A:A.477 Hydrogen bonds: A:I.17, A:C.18, A:A.38, A:G.39, A:G.103, A:T.107, A:T.107, A:A.112, A:S.114, A:S.114, A:V.254, A:V.254, A:N.290, A:E.293, A:N.521, A:T.523, A:T.523 pi-Stacking: A:W.111, A:W.111, A:H.478 pi-Cation interactions: A:H.478

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.2: 14 residues within 4Å: Chain A: R.205, C.216, C.217, G.218, N.219, N.220, N.221, C.222, C.226, P.227, I.228, 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

3 x HEC: HEME C(Covalent)

HEC.3: 23 residues within 4Å: Chain A: 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, T.368, L.376, I.380, V.384, R.386, I.393, M.395, F.398, I.415, V.419 22 PLIP interactions: 21 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:V.342, C:Y.359, C:P.360, C:L.362, C:T.367, C:T.368, C:L.376, C:I.380, C:V.384, C:V.384, C:I.393, C:F.398, C:F.398, C:V.419, A:I.228 Hydrogen bonds: C:R.262, C:N.365, C:T.367 Salt bridges: C:K.257, C:R.262, C:R.386 Metal complexes: C:H.347 HEC.4: 26 residues within 4Å: Chain C: V.195, A.199, H.200, C.201, C.204, H.205, I.225, W.228, R.229, A.230, P.231, I.233, I.241, W.244, L.249, Y.252, L.253, A.264, P.266, M.267, I.286, L.290, T.366, T.367, D.375 Ligands: U10.6 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:V.195, C:A.199, C:W.228, C:I.233, C:I.241, C:W.244, C:W.244, C:L.249, C:Y.252, C:L.253, C:P.266, C:M.267, C:I.286, C:L.290 Hydrogen bonds: C:N.305, C:T.366 Metal complexes: C:H.205 HEC.5: 25 residues within 4Å: Chain C: A.50, D.51, C.52, C.55, H.56, I.71, I.78, Y.79, S.80, T.81, I.83, I.91, Y.94, F.99, A.102, L.103, R.108, Q.113, L.114, Y.115, A.117, M.118, P.119, Y.123, R.161 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:A.50, C:I.78, C:T.81, C:I.83, C:I.91, C:Y.94, C:F.99, C:A.102, C:L.103, C:L.114, C:Y.115, C:A.117, C:Y.123 Salt bridges: C:R.108, C:R.161 Metal complexes: C:H.56

1 x U10: UBIQUINONE-10(Non-covalent)

U10.6: 19 residues within 4Å: Chain C: M.75, Y.115, P.116, L.154, P.157, F.158, S.163, L.164, I.166, W.167, E.203, C.204, R.208, L.211, L.212, I.225, L.447, L.450 Ligands: HEC.4 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Y.115, C:P.116, C:L.154, C:F.158, C:F.158, C:L.164, C:W.167, C:L.211, C:L.212, C:I.225, C:L.447, C:L.447, C:L.450

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukawa, E. et al., Structural and electrochemical elucidation of biocatalytic mechanisms in direct electron transfer-type D-fructose dehydrogenase. Electrochim Acta (2024)

Release Date

2024-05-22

Peptides

Fructose dehydrogenase (N1146A) large subunit: A
Fructose dehydrogenase small subunit: B
Fructose dehydrogenase cytochrome subunit: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Fructose dehydrogenase (N1146A) large subunit

Fructose dehydrogenase small subunit

Fructose dehydrogenase cytochrome subunit

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