SMTL ID : 7ose.1

cytochrome bd-II type oxidase with bound aurachin D

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

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

HEB.1: 24 residues within 4Å: Chain A: K.183, H.186, T.187, A.190, T.234, L.235, G.238, S.241, A.242, V.245, K.252, M.256, F.390, M.393, V.394, G.397, P.433, A.436, I.437, G.440, W.441, M.443, T.444 Ligands: 0NI.4 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:A.190, A:T.234, A:L.235, A:A.242, A:V.245, A:F.390, A:V.394, A:V.394, A:A.436, A:I.437, A:I.437, A:W.441, A:W.441 Hydrogen bonds: A:T.187, A:T.187 Salt bridges: A:K.183, A:K.183, A:K.252 Metal complexes: A:H.186 HEB.2: 19 residues within 4Å: Chain A: R.9, F.12, A.13, A.16, L.17, F.20, F.77, W.81, Y.84, F.92, I.144, N.148, M.151, W.441, E.445, R.448, Q.449, T.459 Ligands: HDD.3 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:R.9, A:F.12, A:A.13, A:A.16, A:L.17, A:F.20, A:F.20, A:F.77, A:W.81, A:Y.84, A:F.92, A:I.144, A:N.148, A:W.441, A:W.441, A:W.441, A:E.445 Hydrogen bonds: A:Q.449 Salt bridges: A:R.9, A:R.448 pi-Cation interactions: A:R.448 HEB.6: 24 residues within 4Å: Chain D: K.183, H.186, T.187, A.190, T.234, L.235, G.238, S.241, A.242, V.245, K.252, M.256, F.390, M.393, V.394, G.397, P.433, A.436, I.437, G.440, W.441, M.443, T.444 Ligands: 0NI.9 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:A.190, D:T.234, D:L.235, D:A.242, D:V.245, D:F.390, D:V.394, D:V.394, D:A.436, D:I.437, D:I.437, D:W.441, D:W.441 Hydrogen bonds: D:T.187, D:T.187 Salt bridges: D:K.183, D:K.183, D:K.252 Metal complexes: D:H.186 HEB.7: 19 residues within 4Å: Chain D: R.9, F.12, A.13, A.16, L.17, F.20, F.77, W.81, Y.84, F.92, I.144, N.148, M.151, W.441, E.445, R.448, Q.449, T.459 Ligands: HDD.8 21 PLIP interactions: 21 interactions with chain D, Hydrophobic interactions: D:R.9, D:F.12, D:A.13, D:A.16, D:L.17, D:F.20, D:F.20, D:F.77, D:W.81, D:Y.84, D:F.92, D:I.144, D:N.148, D:W.441, D:W.441, D:W.441, D:E.445 Hydrogen bonds: D:Q.449 Salt bridges: D:R.9, D:R.448 pi-Cation interactions: D:R.448

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

HDD.3: 23 residues within 4Å: Chain A: H.19, F.20, V.23, L.27, F.63, G.66, V.67, G.70, M.73, E.74, F.77, F.104, E.107, S.108, S.137, S.140, A.141, I.144, W.441 Chain B: E.58, V.62, I.65 Ligands: HEB.2 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.20, A:V.23, A:L.27, A:L.27, A:M.73, A:F.77, A:F.104, A:F.104, A:F.104, A:A.141, A:I.144, A:I.144, A:W.441, B:I.65 Hydrogen bonds: A:S.108, A:S.140 Metal complexes: A:H.19 HDD.8: 23 residues within 4Å: Chain D: H.19, F.20, V.23, L.27, F.63, G.66, V.67, G.70, M.73, E.74, F.77, F.104, E.107, S.108, S.137, S.140, A.141, I.144, W.441 Chain E: E.58, V.62, I.65 Ligands: HEB.7 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain E, Hydrophobic interactions: D:F.20, D:V.23, D:L.27, D:L.27, D:M.73, D:F.77, D:F.104, D:F.104, D:F.104, D:A.141, D:I.144, D:I.144, D:W.441, E:I.65 Hydrogen bonds: D:S.108, D:S.140 Metal complexes: D:H.19

2 x 0NI: Aurachin D(Non-covalent)

0NI.4: 10 residues within 4Å: Chain A: D.239, A.242, E.257, F.269, L.291, L.295, F.390, R.391, V.394 Ligands: HEB.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.242, A:F.269, A:F.269, A:L.291, A:L.295, A:L.295, A:F.390, A:V.394 Hydrogen bonds: A:D.239 0NI.9: 10 residues within 4Å: Chain D: D.239, A.242, E.257, F.269, L.291, L.295, F.390, R.391, V.394 Ligands: HEB.6 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:A.242, D:F.269, D:F.269, D:L.291, D:L.295, D:L.295, D:F.390, D:V.394 Hydrogen bonds: D:D.239

2 x UQ8: Ubiquinone-8(Non-covalent)

UQ8.5: 34 residues within 4Å: Chain B: W.12, G.16, L.19, F.22, M.23, L.71, W.75, A.82, M.90, F.134, G.135, F.138, L.141, L.142, 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, T.304, A.305, G.306, T.308, L.309, V.313 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:W.12, B:F.22, B:L.71, B:W.75, B:A.82, B:F.134, B:F.134, B:F.138, B:F.138, B:L.141, B:L.142, B:L.175, B:F.215, B:A.218, B:L.222, B:V.301, B:I.302, B:T.304, B:A.305, B:T.308 UQ8.10: 34 residues within 4Å: Chain E: W.12, G.16, L.19, F.22, M.23, L.71, W.75, A.82, M.90, F.134, G.135, F.138, L.141, L.142, 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, T.304, A.305, G.306, T.308, L.309, V.313 20 PLIP interactions: 20 interactions with chain E Hydrophobic interactions: E:W.12, E:F.22, E:L.71, E:W.75, E:A.82, E:F.134, E:F.134, E:F.138, E:F.138, E:L.141, E:L.142, E:L.175, E:F.215, E:A.218, E:L.222, E:V.301, E:I.302, E:T.304, E:A.305, E:T.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grauel, A. et al., Structure of Escherichia coli cytochrome bd-II type oxidase with bound aurachin D. Nat Commun (2021)

Release Date

2021-11-17

Peptides

Cytochrome bd-II ubiquinol oxidase subunit 1: AD
Cytochrome bd-II ubiquinol oxidase subunit 2: BE
Putative cytochrome bd-II ubiquinol oxidase subunit AppX: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Membrane

We predict this structure to be a membrane protein.
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Cytochrome bd-II ubiquinol oxidase subunit 1

Cytochrome bd-II ubiquinol oxidase subunit 2

Putative cytochrome bd-II ubiquinol oxidase subunit AppX

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