SMTL ID : 8gy3.1

Cryo-EM Structure of Membrane-Bound Aldehyde Dehydrogenase from Gluconobacter oxydans

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

3 x HEC: HEME C(Covalent)

HEC.1: 23 residues within 4Å: Chain A: G.55, Y.56, C.57, C.60, H.61, M.78, S.88, I.90, W.101, F.106, M.110, A.115, L.121, Y.122, A.124, F.125, P.126, F.130, L.141, L.145, R.167, H.206 Ligands: U10.4 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:I.90, A:W.101, A:W.101, A:F.106, A:F.106, A:L.121, A:F.125, A:F.130, A:F.130, A:L.145 Hydrogen bonds: A:S.88, A:Y.122 Salt bridges: A:R.167 Metal complexes: A:H.61 HEC.2: 24 residues within 4Å: Chain A: Y.56, E.205, H.206, C.207, C.210, H.211, I.231, W.234, I.235, A.236, P.237, L.239, N.243, T.245, W.249, L.254, Y.257, L.258, A.270, P.272, M.273, Y.296, N.363 Ligands: U10.4 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:Y.56, A:E.205, A:I.231, A:A.236, A:P.237, A:L.239, A:L.239, A:W.249, A:L.254, A:Y.257, A:L.258, A:L.258, A:P.272, A:Y.296 Hydrogen bonds: A:N.243, A:Y.257, A:N.363 Salt bridges: A:H.266 Metal complexes: A:H.211 HEC.3: 26 residues within 4Å: Chain A: G.267, S.268, A.340, C.341, C.344, H.345, G.355, P.357, L.359, N.362, A.364, L.373, V.376, M.377, I.381, T.382, G.386, Q.387, I.390, S.391, M.392, P.393, F.395, L.399 Chain B: A.55, T.56 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:P.357, A:L.359, A:L.359, A:A.364, A:L.373, A:V.376, A:I.381, A:L.399 Hydrogen bonds: A:S.268, A:S.268, A:S.268, A:G.386, A:Q.387 Metal complexes: A:H.345

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

U10.4: 21 residues within 4Å: Chain A: E.59, C.60, T.80, F.82, I.85, Y.122, P.123, A.124, I.164, I.169, G.170, Q.171, F.173, W.174, H.206, A.209, R.214, L.217, D.232 Ligands: HEC.1, HEC.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.80, A:F.82, A:F.82, A:F.82, A:Y.122, A:I.164, A:A.209

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.5: 10 residues within 4Å: Chain B: G.38, C.39, G.40, G.42, E.43, C.44, G.45, C.47, R.57, C.59 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.39, B:C.44, B:C.47, B:C.59 FES.6: 9 residues within 4Å: Chain B: Q.96, C.97, G.98, C.100, Q.101, C.132, R.133, C.134 Chain C: L.362 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.97, B:C.100, B:C.132, B:C.134

1 x PCD: (MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)(Non-covalent)

PCD.7: 37 residues within 4Å: Chain B: Q.96, C.134 Chain C: M.77, G.78, Q.79, H.80, V.81, A.84, G.118, G.119, S.120, W.121, S.122, V.123, Q.383, G.412, G.413, F.414, G.415, L.418, W.537, L.538, R.539, V.541, A.659, T.661, I.662, V.663, D.664, A.668, Q.671, P.725, T.726, G.727, L.728, G.729, E.730 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:L.728 Hydrogen bonds: C:G.78, C:Q.79, C:H.80, C:G.119, C:S.122, C:S.122, C:V.123, C:Q.383, C:G.413, C:F.414, C:T.661, C:V.663, C:D.664, C:D.664, C:A.668, C:Q.671, C:Q.671, C:T.726, C:L.728, C:G.729, C:E.730

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adachi, T. et al., Experimental and Theoretical Insights into Bienzymatic Cascade for Mediatorless Bioelectrochemical Ethanol Oxidation with Alcohol and Aldehyde Dehydrogenases. Acs Catalysis (2023)

Release Date

2023-08-02

Peptides

Cytochrome c subunit of aldehyde dehydrogenase: A
Small subunit of aldehyde dehydrogenase: B
Large subunit of aldehyde dehydrogenase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c subunit of aldehyde dehydrogenase

Small subunit of aldehyde dehydrogenase

Large subunit of aldehyde dehydrogenase