SMTL ID : 6rko.1

Cryo-EM structure of the E. coli cytochrome bd-I oxidase at 2.68 A resolution

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

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

UQ8.1: 30 residues within 4Å: Chain A: W.12, V.15, G.16, L.19, F.22, A.23, L.64, L.71, V.78, F.86, I.134, F.138, L.141, L.142, S.176, M.179, F.215, A.218, G.219, M.223, F.259, W.266, P.269, I.302, I.303, L.304, T.305, A.306, A.309, V.314 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:W.12, A:V.15, A:L.19, A:L.19, A:A.23, A:L.64, A:L.71, A:V.78, A:F.86, A:I.134, A:I.134, A:I.134, A:F.138, A:F.138, A:L.141, A:L.142, A:L.142, A:I.302, A:I.303, A:I.303, A:T.305, A:A.306, A:A.309, A:V.314

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

POV.2: 14 residues within 4Å: Chain A: V.17, G.21, T.25, M.190, R.191, A.289, F.292, V.293, S.296, L.297, Y.359, F.363, G.364, R.365 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.25, A:F.292, A:V.293, A:Y.359, A:F.363, A:F.363 Salt bridges: A:R.191, A:R.365 POV.3: 5 residues within 4Å: Chain A: E.5, F.9, L.13, H.237, W.328 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.13, A:L.13 Salt bridges: A:H.237 POV.4: 14 residues within 4Å: Chain B: L.21, W.421, A.425, Y.428, P.431, L.432, W.434, I.435, E.438 Chain C: F.7, T.11, I.14, V.22 Ligands: POV.5 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.21, B:P.431, B:P.431, B:L.432, B:W.434, B:I.435, B:E.438, B:E.438, C:I.14, C:I.14, C:V.22 Hydrogen bonds: B:Y.428 POV.5: 21 residues within 4Å: Chain B: L.21, F.22, N.62, F.198, I.202, W.205, K.209, R.211, L.427, P.431, W.434, E.489, L.490, M.493, F.494, A.497, R.498 Chain C: F.7, T.11, V.15 Ligands: POV.4 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.21, B:F.22, B:F.198, B:I.202, B:W.205, B:L.427, B:P.431, B:W.434, B:W.434, B:L.490, B:F.494, B:F.494, B:A.497, C:T.11, C:V.15 Salt bridges: B:R.498, B:R.498

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

HDD.6: 23 residues within 4Å: Chain A: D.58, I.65 Chain B: H.19, V.23, T.26, L.27, F.63, G.66, V.67, G.70, M.73, E.74, F.77, F.104, E.107, S.108, S.140, A.141, I.144, T.187, W.441 Ligands: HEB.7, OXY.9 24 PLIP interactions: 21 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:V.23, B:V.23, B:T.26, B:L.27, B:M.73, B:E.74, B:F.77, B:F.104, B:F.104, B:F.104, B:F.104, B:A.141, B:I.144, B:I.144, B:I.144, B:T.187, B:W.441, A:I.65, A:I.65 Hydrogen bonds: B:E.107, B:S.108, B:S.140 Metal complexes: B:H.19 Water bridges: A:D.58

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

HEB.7: 24 residues within 4Å: Chain B: R.9, F.12, A.13, A.16, M.17, F.20, F.77, W.81, Y.84, F.92, I.144, A.147, N.148, M.151, E.438, W.441, E.445, Y.446, R.448, Q.449, W.451, T.459 Chain C: A.26 Ligands: HDD.6 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:F.12, B:F.12, B:F.20, B:F.77, B:F.77, B:W.81, B:W.81, B:F.92, B:I.144, B:A.147, B:N.148, B:W.441, B:W.441, B:W.441, B:W.441, B:E.445 Hydrogen bonds: B:T.459 Salt bridges: B:R.9, B:R.448 pi-Stacking: B:F.12 pi-Cation interactions: B:R.448 Metal complexes: B:E.445 HEB.8: 18 residues within 4Å: Chain B: Q.152, K.183, H.186, T.187, S.190, V.234, I.235, D.239, K.252, F.390, M.393, V.394, G.397, A.436, V.437, G.440, W.441, A.444 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:V.234, B:I.235, B:D.239, B:V.394, B:V.394, B:A.436, B:V.437, B:V.437, B:W.441, B:W.441, B:A.444 Hydrogen bonds: B:D.239 Salt bridges: B:K.183, B:K.183, B:K.252 pi-Stacking: B:W.441 pi-Cation interactions: B:H.186, B:H.186 Metal complexes: B:H.186

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.9: 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

Safarian, S. et al., Active site rearrangement and structural divergence in prokaryotic respiratory oxidases. Science (2019)

Release Date

2019-10-16

Peptides

Cytochrome bd-I ubiquinol oxidase subunit 2: A
Cytochrome bd-I ubiquinol oxidase subunit 1: B
Uncharacterized protein YnhF: C
Cytochrome bd-I ubiquinol oxidase subunit X: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
H

D
X

Membrane

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

Cytochrome bd-I ubiquinol oxidase subunit 1

Uncharacterized protein YnhF

Cytochrome bd-I ubiquinol oxidase subunit X

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