SMTL ID : 8f6c.1

E. coli cytochrome bo3 ubiquinol oxidase dimer

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.46 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 21 residues within 4Å: Chain A: F.73, A.76, M.79, R.80, Q.83, F.103, H.106, G.107, M.110, I.111, G.169, W.170, L.414, I.417, F.420, H.421, I.424, W.460, F.468, R.481, R.482 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:F.73, A:A.76, A:M.110, A:I.111, A:I.111, A:W.170, A:I.417, A:F.420, A:I.424, A:W.460, A:F.468 Hydrogen bonds: A:Q.83, A:W.170, A:R.482 Salt bridges: A:R.481, A:R.482 pi-Stacking: A:H.106, A:F.420, A:H.421 Metal complexes: A:H.106 HEM.7: 21 residues within 4Å: Chain E: F.73, A.76, M.79, R.80, Q.83, F.103, H.106, G.107, M.110, I.111, G.169, W.170, L.414, I.417, F.420, H.421, I.424, W.460, F.468, R.481, R.482 20 PLIP interactions: 20 interactions with chain E, Hydrophobic interactions: E:F.73, E:A.76, E:M.110, E:I.111, E:I.111, E:W.170, E:I.417, E:F.420, E:I.424, E:W.460, E:F.468 Hydrogen bonds: E:Q.83, E:W.170, E:R.482 Salt bridges: E:R.481, E:R.482 pi-Stacking: E:H.106, E:F.420, E:H.421 Metal complexes: E:H.106

2 x HEO: HEME O(Non-covalent)

HEO.2: 31 residues within 4Å: Chain A: W.170, W.280, V.287, Y.288, I.291, H.333, H.334, I.355, A.356, T.359, G.360, I.363, F.391, G.395, G.398, V.399, L.401, A.402, D.407, H.411, L.416, H.419, F.420, V.423, I.424, V.428, R.481 Chain B: M.28, V.31, I.77 Ligands: CU.3 25 PLIP interactions: 23 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:W.280, A:V.287, A:V.287, A:I.291, A:I.291, A:A.356, A:I.363, A:F.391, A:F.391, A:V.399, A:L.401, A:L.401, A:L.416, A:F.420, A:V.423, A:I.424, A:V.428, B:V.31, B:I.77 Hydrogen bonds: A:Y.288, A:H.333 Salt bridges: A:H.411, A:R.481 pi-Stacking: A:H.333 Metal complexes: A:H.419 HEO.8: 31 residues within 4Å: Chain E: W.170, W.280, V.287, Y.288, I.291, H.333, H.334, I.355, A.356, T.359, G.360, I.363, F.391, G.395, G.398, V.399, L.401, A.402, D.407, H.411, L.416, H.419, F.420, V.423, I.424, V.428, R.481 Chain F: M.28, V.31, I.77 Ligands: CU.9 25 PLIP interactions: 23 interactions with chain E, 2 interactions with chain F, Hydrophobic interactions: E:W.280, E:V.287, E:V.287, E:I.291, E:I.291, E:A.356, E:I.363, E:F.391, E:F.391, E:V.399, E:L.401, E:L.401, E:L.416, E:F.420, E:V.423, E:I.424, E:V.428, F:V.31, F:I.77 Hydrogen bonds: E:Y.288, E:H.333 Salt bridges: E:H.411, E:R.481 pi-Stacking: E:H.333 Metal complexes: E:H.419

2 x CU: COPPER (II) ION(Non-covalent)

CU.3: 4 residues within 4Å: Chain A: H.284, H.333, H.334 Ligands: HEO.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.284, A:H.333, A:H.334 CU.9: 4 residues within 4Å: Chain E: H.284, H.333, H.334 Ligands: HEO.8 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.284, E:H.333, E:H.334

6 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.4: 18 residues within 4Å: Chain A: F.138, P.139, F.140, L.141, L.144, Q.195, I.199, F.602, M.621, W.625, K.628, V.634 Chain C: K.5, G.8, F.9, Y.12 Ligands: 3PE.5, 3PE.6 12 PLIP interactions: 3 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:Y.12, C:Y.12, C:Y.12, A:F.138, A:F.140, A:L.141, A:L.144, A:F.602, A:W.625, A:W.625, A:W.625 Hydrogen bonds: A:F.140 3PE.5: 7 residues within 4Å: Chain A: A.251, T.254, Y.258, F.602, W.611, I.615 Ligands: 3PE.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.251, A:T.254, A:Y.258, A:F.602, A:W.611, A:W.611, A:W.611, A:I.615 3PE.6: 16 residues within 4Å: Chain A: A.251, F.618, I.622, W.625, S.629 Chain C: K.5, F.9, Y.12, T.125, H.129, S.132, W.136, V.139, T.152, R.156 Ligands: 3PE.4 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:A.251, A:F.618, A:I.622, A:W.625, A:W.625, A:W.625, C:F.9, C:W.136, C:V.139 Hydrogen bonds: A:W.625 Salt bridges: C:K.5, C:R.156, C:R.156 3PE.10: 18 residues within 4Å: Chain E: F.138, P.139, F.140, L.141, L.144, Q.195, I.199, F.602, M.621, W.625, K.628, V.634 Chain G: K.5, G.8, F.9, Y.12 Ligands: 3PE.11, 3PE.12 12 PLIP interactions: 9 interactions with chain E, 3 interactions with chain G Hydrophobic interactions: E:F.138, E:F.140, E:L.141, E:L.144, E:F.602, E:W.625, E:W.625, E:W.625, G:Y.12, G:Y.12, G:Y.12 Hydrogen bonds: E:F.140 3PE.11: 7 residues within 4Å: Chain E: A.251, T.254, Y.258, F.602, W.611, I.615 Ligands: 3PE.10 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:A.251, E:T.254, E:Y.258, E:F.602, E:W.611, E:W.611, E:W.611, E:I.615 3PE.12: 16 residues within 4Å: Chain E: A.251, F.618, I.622, W.625, S.629 Chain G: K.5, F.9, Y.12, T.125, H.129, S.132, W.136, V.139, T.152, R.156 Ligands: 3PE.10 13 PLIP interactions: 6 interactions with chain G, 7 interactions with chain E Hydrophobic interactions: G:F.9, G:W.136, G:V.139, E:A.251, E:F.618, E:I.622, E:W.625, E:W.625, E:W.625 Salt bridges: G:K.5, G:R.156, G:R.156 Hydrogen bonds: E:W.625

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, Y. et al., Monomer and dimer structures of cytochrome bo 3 ubiquinol oxidase from Escherichia coli. Protein Sci. (2023)

Release Date

2022-11-30

Peptides

Cytochrome bo(3) ubiquinol oxidase subunit 1: AE
Cytochrome bo(3) ubiquinol oxidase subunit 2: BF
Cytochrome bo(3) ubiquinol oxidase subunit 3: CG
Cytochrome bo(3) ubiquinol oxidase subunit 4: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

Membrane

We predict this structure to be a membrane protein.
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Cytochrome bo(3) ubiquinol oxidase subunit 1

Cytochrome bo(3) ubiquinol oxidase subunit 2

Cytochrome bo(3) ubiquinol oxidase subunit 3

Cytochrome bo(3) ubiquinol oxidase subunit 4

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