SMTL ID : 8gy2.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

4 x HEC: HEME C(Covalent)

HEC.1: 23 residues within 4Å: Chain A: R.92, A.137, D.138, F.652, C.653, C.656, H.657, L.667, P.668, L.670, S.673, A.675, F.682, L.685, V.686, L.691, Y.694, M.696, F.699 Chain B: M.354, P.389, S.390, A.391 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:D.138, A:F.652, A:L.667, A:P.668, A:L.670, A:A.675, A:F.682, A:L.685, A:V.686, A:V.686, A:Y.694, A:F.699 pi-Stacking: A:H.657, A:H.657 pi-Cation interactions: A:H.657 Metal complexes: A:H.657 Hydrogen bonds: B:S.390 HEC.4: 23 residues within 4Å: Chain B: S.54, D.55, C.56, C.59, H.60, I.74, T.84, I.86, I.94, Y.97, F.102, L.106, R.111, V.117, Y.118, A.120, M.121, P.122, F.126, M.137, F.141, R.164, H.203 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:I.74, B:T.84, B:I.86, B:I.94, B:F.102, B:L.106, B:A.120, B:F.126, B:F.126, B:F.141 Hydrogen bonds: B:Y.97, B:Y.97, B:Y.118 Salt bridges: B:R.111, B:R.164 Metal complexes: B:H.60 HEC.5: 20 residues within 4Å: Chain B: H.203, C.204, C.207, H.208, W.238, I.239, A.240, P.241, L.243, W.254, F.262, L.263, S.271, A.272, V.273, F.274, M.277, V.280, P.362, V.363 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:W.238, B:P.241, B:L.243, B:W.254, B:F.262, B:L.263, B:F.274, B:M.277, B:V.280, B:V.363 Hydrogen bonds: B:S.271, B:F.274 pi-Stacking: B:H.208, B:H.208 Metal complexes: B:H.208 HEC.6: 27 residues within 4Å: Chain B: A.272, V.273, F.274, N.339, C.340, I.342, C.343, H.344, M.354, F.355, P.356, L.358, N.361, V.363, L.372, V.375, V.376, G.380, L.382, V.392, A.393, M.394, P.395, F.397, M.413, Y.460, F.466 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:A.272, B:F.274, B:N.339, B:I.342, B:F.355, B:P.356, B:L.358, B:V.363, B:L.372, B:V.375, B:V.376, B:V.392, B:F.466 Hydrogen bonds: B:A.272, B:V.273, B:N.361 Metal complexes: B:H.344

1 x PQQ: PYRROLOQUINOLINE QUINONE(Covalent)

PQQ.2: 20 residues within 4Å: Chain A: E.95, C.141, C.142, R.147, D.197, G.213, A.214, E.215, T.277, W.279, N.297, D.342, K.369, E.426, L.427, N.431, F.432, W.523, I.588 Ligands: CA.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.279, A:W.279, A:I.588 Hydrogen bonds: A:G.213, A:A.214, A:E.215, A:N.297, A:K.369, A:N.431 Salt bridges: A:R.147, A:R.147

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: E.215, N.297, D.342 Ligands: PQQ.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.215, A:E.215, A:D.342

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

U10.7: 17 residues within 4Å: Chain B: A.58, C.59, L.72, I.74, S.76, P.77, Y.118, P.119, A.120, L.167, W.170, E.206, C.207, R.211, M.215, I.235, D.279 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.74, B:P.77, B:P.119

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

Alcohol dehydrogenase (quinone), dehydrogenase subunit: A
Alcohol dehydrogenase (quinone), cytochrome c subunit: B
Small subunit of alcohol dehydrogenase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Alcohol dehydrogenase (quinone), dehydrogenase subunit

Alcohol dehydrogenase (quinone), cytochrome c subunit

Small subunit of alcohol dehydrogenase