SMTL ID : 8xcm.1

Cryo-EM Structure of Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus variant-N1146Q

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: 37 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, I.101, 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.289, N.290, E.293, L.297, Q.477, H.478, T.510, N.521, S.522, T.523, M.526 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:Y.64, A:Q.477 Hydrogen bonds: A:A.15, A:I.17, A:C.18, A:A.38, A:G.39, A:G.103, A:G.103, A:G.106, A:T.107, A:T.108, A:T.108, A:A.112, A:S.114, A:S.114, A:V.254, A:V.254, A:Q.477, A:T.510, A:N.521, A:S.522, A:T.523, A:T.523 pi-Stacking: A:H.110, A:W.111, A:W.111, A:H.478

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

F3S.2: 13 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, A.230, G.342 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: 26 residues within 4Å: Chain A: I.228 Chain C: R.262, A.264, V.342, C.343, C.346, H.347, Y.358, Y.359, P.360, L.362, N.365, T.367, T.368, L.376, S.379, I.380, V.384, R.386, I.393, M.395, P.396, F.398, I.415, V.419 Ligands: HEC.4 24 PLIP interactions: 23 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:R.262, C:R.262, C:V.342, C:Y.359, C:P.360, C:L.362, C:T.368, C:L.376, C:I.380, C:V.384, C:V.384, C:P.396, C:F.398, C:I.415, C:V.419, A:I.228 Hydrogen bonds: C:R.262, C:N.365, C:S.379, C:S.379 Salt bridges: C:K.257, C:R.262, C:R.386 Metal complexes: C:H.347 HEC.4: 25 residues within 4Å: Chain C: A.199, H.200, C.201, C.204, H.205, I.225, W.228, R.229, A.230, P.231, I.233, I.241, L.249, Y.252, L.253, A.264, P.266, M.267, L.275, L.290, T.366, T.367, Q.370, D.375 Ligands: HEC.3 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:A.199, C:W.228, C:A.230, C:P.231, C:I.233, C:I.241, C:L.249, C:Y.252, C:L.253, C:P.266, C:P.266, C:M.267, C:L.275, C:L.290 Hydrogen bonds: C:N.305, C:T.366, C:Q.370 Metal complexes: C:H.205 HEC.5: 20 residues within 4Å: Chain C: A.50, D.51, C.52, C.55, H.56, I.71, I.78, S.80, T.81, I.83, F.99, A.102, L.103, R.108, L.114, Y.115, A.117, M.118, Y.123, R.161 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:A.50, C:I.71, C:T.81, C:I.83, C:F.99, C:A.102, C:L.103, C:Y.115, C:A.117 Salt bridges: C:R.108, C:R.161 Metal complexes: C:H.56

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

U10.6: 17 residues within 4Å: Chain C: S.73, M.75, Y.115, P.116, P.157, F.158, S.163, I.166, W.167, E.203, C.204, R.208, L.212, I.225, P.266, L.447, L.450 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.115, C:P.116, C:F.158, C:W.167, C:L.212, C:L.212, C:I.225, C:P.266, 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 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 large subunit

Fructose dehydrogenase small subunit

Fructose dehydrogenase cytochrome subunit

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