SMTL ID : 7oy2.1

High resolution structure of cytochrome bd-II oxidase from E. coli

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x CDN: CARDIOLIPIN(Non-covalent)

CDN.1: 16 residues within 4Å: Chain A: V.21, I.24, S.25, L.190, R.286, P.287, G.288, W.289, F.291, L.292, S.295, L.351, T.354, L.355, Y.358, W.362 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.21, A:I.24, A:L.190, A:F.291, A:L.292, A:L.351, A:T.354, A:Y.358, A:Y.358, A:Y.358, A:Y.358, A:W.362, A:W.362 Hydrogen bonds: A:G.288, A:W.289, A:W.289 Salt bridges: A:R.286

1 x DK8: 2-[(2~{E},6~{E},10~{Z},14~{E},18~{E},22~{E},26~{E})-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaenyl]naphthalene-1,4-dione(Non-covalent)

DK8.2: 37 residues within 4Å: Chain A: W.12, G.16, L.19, F.22, M.23, L.64, L.71, W.75, V.78, A.82, F.83, F.134, G.135, A.137, F.138, L.141, C.172, L.175, S.176, M.179, F.215, A.218, G.219, L.222, M.255, F.258, W.265, P.268, V.301, I.302, F.303, T.304, A.305, G.306, T.308, L.309, V.313 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: A:W.12, A:L.19, A:F.22, A:L.64, A:L.71, A:W.75, A:V.78, A:F.83, A:F.134, A:F.134, A:F.134, A:F.134, A:A.137, A:F.138, A:F.138, A:F.138, A:F.138, A:L.141, A:L.141, A:F.215, A:A.218, A:L.222, A:W.265, A:P.268, A:P.268, A:V.301, A:I.302, A:F.303, A:T.304, A:L.309, A:V.313 Hydrogen bonds: A:G.219, A:T.308 pi-Stacking: A:F.258

1 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.3: 15 residues within 4Å: Chain B: L.21, F.22, N.62, W.205, R.209, L.427, W.428, L.430, P.431, W.434, I.435, E.438, M.493, A.497, R.498 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.21, B:F.22, B:W.205, B:W.205, B:L.430, B:L.430, B:P.431, B:W.434, B:W.434, B:E.438, B:A.497, B:R.498 Salt bridges: B:R.209, B:R.498, B:R.498

2 x HEB: HEME B/C(Non-covalent)

HEB.4: 21 residues within 4Å: Chain B: R.9, F.12, A.13, A.16, L.17, F.20, F.77, Y.84, F.92, I.144, A.147, N.148, M.151, W.441, E.445, F.446, R.448, Q.449, A.452, T.459 Ligands: HDD.6 25 PLIP interactions: 25 interactions with chain B, Hydrophobic interactions: B:F.12, B:F.12, B:A.13, B:A.16, B:L.17, B:F.20, B:F.20, B:F.77, B:Y.84, B:F.92, B:I.144, B:I.144, B:A.147, B:W.441, B:W.441, B:W.441, B:E.445, B:A.452, B:T.459 Hydrogen bonds: B:Q.449, B:T.459 Salt bridges: B:R.9, B:R.448 pi-Cation interactions: B:R.448 Metal complexes: B:E.445 HEB.5: 24 residues within 4Å: Chain B: K.183, H.186, T.187, A.190, V.193, I.231, T.234, L.235, G.238, D.239, S.241, A.242, V.245, K.252, F.390, M.393, V.394, G.397, A.436, I.437, G.440, W.441, M.443, T.444 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:A.190, B:V.193, B:I.231, B:T.234, B:L.235, B:L.235, B:F.390, B:F.390, B:V.394, B:A.436, B:I.437, B:W.441, B:W.441 Hydrogen bonds: B:T.444 Salt bridges: B:K.183, B:K.183, B:K.252 pi-Stacking: B:H.186, B:W.441 Metal complexes: B:H.186

1 x HDD: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE(Non-covalent)

HDD.6: 28 residues within 4Å: Chain A: E.58, V.62, I.65 Chain B: F.12, H.19, F.20, V.23, T.26, L.27, F.63, V.67, G.70, L.71, M.73, E.74, F.77, F.104, E.107, S.108, S.137, S.140, A.141, I.144, L.145, T.187, W.441 Ligands: HEB.4, OXY.7 30 PLIP interactions: 27 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:F.12, B:F.20, B:V.23, B:V.23, B:T.26, B:L.27, B:L.27, B:F.63, B:M.73, B:E.74, B:F.77, B:F.104, B:F.104, B:F.104, B:A.141, B:I.144, B:I.144, B:I.144, B:L.145, B:L.145, B:T.187, B:W.441, A:I.65, A:I.65 Hydrogen bonds: B:F.104, B:E.107, B:S.108, B:S.140, A:E.58 Metal complexes: B:H.19

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.7: 5 residues within 4Å: Chain B: E.99, F.104, S.140, I.144 Ligands: HDD.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grund, T.N. et al., Mechanistic and structural diversity between cytochrome bd isoforms of Escherichia coli . Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-12-15

Peptides

Cytochrome bd-II ubiquinol oxidase subunit 2: A
Cytochrome bd-II ubiquinol oxidase subunit 1: B
Putative cytochrome bd-II ubiquinol oxidase subunit AppX: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
X

Membrane

We predict this structure to be a membrane protein.
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Cytochrome bd-II ubiquinol oxidase subunit 2

Cytochrome bd-II ubiquinol oxidase subunit 1

Putative cytochrome bd-II ubiquinol oxidase subunit AppX

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