SMTL ID : 8smr.1

cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-1-1-1-mer

Ligands

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.1: 9 residues within 4Å: Chain A: C.122, H.124, L.125, C.127, C.150, C.152, H.153, S.155, P.168 7 PLIP interactions: 7 interactions with chain A, Metal complexes: A:C.122, A:H.124, A:H.124, A:H.124, A:C.127, A:C.150, A:H.153 FES.9: 8 residues within 4Å: Chain F: C.122, H.124, C.127, C.150, C.152, H.153, S.155, P.168 5 PLIP interactions: 5 interactions with chain F, Metal complexes: F:C.122, F:H.124, F:H.124, F:C.150, F:H.153

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

HEM.2: 22 residues within 4Å: Chain B: Y.35, G.38, S.39, A.41, L.42, F.94, V.98, H.101, M.102, R.104, S.110, V.118, W.119, G.122, M.123, I.125, Y.126, L.129, H.203, L.207, S.212, N.213 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:A.41, B:L.42, B:L.42, B:F.94, B:V.98, B:V.98, B:V.118, B:W.119, B:W.119, B:I.125, B:Y.126, B:L.129, B:L.207, B:L.207 Hydrogen bonds: B:Y.35, B:G.38, B:S.110, B:N.213 Salt bridges: B:H.101, B:R.104, B:R.104 pi-Cation interactions: B:R.104 Metal complexes: B:H.203 HEM.3: 26 residues within 4Å: Chain B: Q.48, I.49, G.52, I.53, L.55, T.56, F.59, R.84, H.87, S.88, A.91, F.94, L.129, E.132, G.136, Y.137, L.139, P.140, H.188, V.189, P.193, L.196, L.270, N.274, Y.292 Chain G: I.190 22 PLIP interactions: 21 interactions with chain B, 1 interactions with chain G, Hydrophobic interactions: B:Q.48, B:I.53, B:L.55, B:F.59, B:F.59, B:F.94, B:L.129, B:E.132, B:L.139, B:L.139, B:P.140, B:V.189, B:V.189, B:P.193, B:L.196, G:I.190 Hydrogen bonds: B:S.88, B:N.274 Salt bridges: B:R.84, B:R.84 Metal complexes: B:H.87, B:H.188 HEM.11: 25 residues within 4Å: Chain G: Y.35, F.37, G.38, S.39, A.41, L.42, F.94, V.98, H.101, M.102, R.104, S.110, R.115, V.118, W.119, G.122, M.123, I.125, Y.126, L.129, V.200, H.203, L.207, S.212, N.213 25 PLIP interactions: 25 interactions with chain G, Hydrophobic interactions: G:A.41, G:L.42, G:F.94, G:V.98, G:V.98, G:V.118, G:W.119, G:W.119, G:W.119, G:I.125, G:Y.126, G:L.129, G:V.200, G:L.207, G:L.207 Hydrogen bonds: G:G.38, G:S.39, G:S.110, G:N.213 Salt bridges: G:H.101, G:R.104, G:R.104, G:R.115 pi-Cation interactions: G:R.104 Metal complexes: G:H.203 HEM.12: 24 residues within 4Å: Chain B: I.190 Chain G: Q.48, I.49, G.52, I.53, L.55, T.56, F.59, R.84, H.87, A.91, F.94, L.129, E.132, G.136, Y.137, L.139, P.140, H.188, V.189, P.193, L.196, L.270, Y.292 19 PLIP interactions: 18 interactions with chain G, 1 interactions with chain B, Hydrophobic interactions: G:Q.48, G:I.53, G:L.55, G:F.59, G:F.59, G:F.94, G:L.129, G:E.132, G:L.139, G:L.139, G:V.189, G:V.189, G:P.193, G:L.196, B:I.190 Salt bridges: G:R.84, G:R.84 Metal complexes: G:H.87, G:H.188 HEM.20: 27 residues within 4Å: Chain K: M.23, G.26, V.27, I.29, A.30, R.51, H.54, T.55, V.58, I.59, E.116, Y.117, D.334, T.336, I.337, V.340, H.341, A.344, L.345, V.348, Y.389, R.431, G.435, F.438 Chain L: K.103 Ligands: CA.19, HEM.21 21 PLIP interactions: 20 interactions with chain K, 1 interactions with chain L, Hydrophobic interactions: K:I.29, K:A.30, K:T.55, K:V.58, K:Y.117, K:I.337, K:I.337, K:V.340, K:V.340, K:A.344, K:V.348, K:Y.389, K:F.438 Hydrogen bonds: K:Y.117, K:D.334 Salt bridges: K:R.51, K:R.51, K:R.431, L:K.103 pi-Stacking: K:Y.389 Metal complexes: K:H.54 HEM.21: 28 residues within 4Å: Chain K: E.116, Y.117, W.197, V.204, L.208, T.209, H.251, H.252, S.270, L.273, S.277, T.315, G.318, P.319, M.321, A.322, N.327, H.331, T.336, H.339, V.340, G.343, W.347, V.348 Chain L: S.102 Ligands: CU.17, CA.19, HEM.20 17 PLIP interactions: 17 interactions with chain K, Hydrophobic interactions: K:V.204, K:L.208, K:L.208, K:L.273, K:T.315, K:P.319, K:M.321, K:V.340, K:V.340, K:V.348 Hydrogen bonds: K:H.252, K:N.327, K:T.336 Salt bridges: K:H.331 pi-Cation interactions: K:H.201, K:H.252 Metal complexes: K:H.339

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

U10.4: 27 residues within 4Å: Chain A: G.20, A.24, A.27, A.28, F.31 Chain B: F.134, G.148, V.151, I.152, L.155, F.156, W.169, I.170, I.287, A.288, P.289, F.293, F.296, Y.297, L.300, M.313 Chain G: L.43, L.50, W.54, V.248, L.252 Chain H: F.220 16 PLIP interactions: 4 interactions with chain G, 9 interactions with chain B, 2 interactions with chain A, 1 interactions with chain H Hydrophobic interactions: G:L.43, G:W.54, G:V.248, G:L.252, B:F.134, B:L.155, B:F.156, B:I.170, B:F.293, B:F.296, B:Y.297, B:L.300, A:A.27, A:F.31, H:F.220 pi-Stacking: B:Y.297 U10.13: 27 residues within 4Å: Chain B: L.43, L.50, W.54, V.248, L.252 Chain C: F.220 Chain F: G.20, G.23, A.24, A.27, A.28, W.35, H.153 Chain G: M.130, F.134, G.148, V.151, I.152, F.156, W.169, I.170, I.287, A.288, P.289, Y.297, L.300, M.313 18 PLIP interactions: 5 interactions with chain B, 3 interactions with chain F, 9 interactions with chain G, 1 interactions with chain C Hydrophobic interactions: B:L.43, B:L.50, B:W.54, B:V.248, B:L.252, F:A.27, F:W.35, F:W.35, G:F.134, G:F.134, G:V.151, G:I.152, G:F.156, G:I.170, G:Y.297, G:Y.297, G:L.300, C:F.220

2 x I7Y: (2R)-2-(methoxymethyl)-4-{[(25R)-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside(Non-covalent)

I7Y.5: 12 residues within 4Å: Chain B: A.302, V.303, P.304, M.308, V.311, A.312, A.315, R.372, T.375, V.376, F.379, I.383 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.302, B:V.303, B:V.303, B:A.312, B:A.315, B:T.375, B:F.379, B:F.379, B:F.379, B:F.379, B:I.383 I7Y.10: 17 residues within 4Å: Chain F: Q.89, H.156, Y.164, K.165, G.166 Chain G: A.302, V.303, P.304, M.308, V.311, A.312, A.315, R.372, T.375, V.376, F.379, I.383 13 PLIP interactions: 9 interactions with chain G, 4 interactions with chain F Hydrophobic interactions: G:V.303, G:V.303, G:A.312, G:A.315, G:T.375, G:F.379, G:F.379, G:F.379, G:I.383 Hydrogen bonds: F:D.143, F:D.143, F:H.156, F:G.166

9 x HEC: HEME C(Covalent)

HEC.6: 26 residues within 4Å: Chain B: E.276 Chain C: Y.26, C.27, C.30, H.31, F.80, A.82, A.83, P.84, P.85, L.87, V.90, R.94, W.98, L.99, Y.102, L.103, F.121, V.124, G.125, M.126, V.129, L.130, L.191 Chain D: G.112, C.113 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:Y.26, C:F.80, C:F.80, C:A.82, C:P.84, C:P.85, C:W.98, C:W.98, C:L.99, C:Y.102, C:L.103, C:V.124, C:M.126, C:V.129, C:L.130 Hydrogen bonds: C:G.125 Salt bridges: C:R.94, B:K.282 Metal complexes: C:H.31 HEC.7: 28 residues within 4Å: Chain C: M.71, F.80 Chain D: Y.39, K.42, Q.43, M.107, P.108, A.109, C.110, C.113, H.114, F.126, P.127, L.129, Y.136, V.137, Q.140, L.141, F.144, R.149, N.151, D.152, I.157, M.158, I.161, L.165, I.173 Ligands: HEC.8 24 PLIP interactions: 1 interactions with chain C, 23 interactions with chain D, Hydrophobic interactions: C:F.80, D:Y.39, D:P.108, D:F.126, D:F.126, D:L.129, D:L.129, D:V.137, D:F.144, D:D.152, D:I.157, D:I.157, D:I.161, D:I.161, D:L.165 Hydrogen bonds: D:Q.35, D:Q.43, D:Q.132, D:N.151 Salt bridges: D:K.42, D:R.52, D:R.149, D:R.149 Metal complexes: D:H.114 HEC.8: 23 residues within 4Å: Chain D: V.13, C.14, C.17, H.18, F.29, P.30, L.32, Y.39, L.40, Q.43, M.44, R.52, V.54, E.56, M.57, L.60, L.61, L.64, I.72, Y.136, K.139, Q.140 Ligands: HEC.7 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:F.29, D:F.29, D:P.30, D:L.32, D:L.40, D:Q.43, D:V.54, D:E.56, D:E.56, D:L.60, D:L.64, D:I.72, D:Y.136 Hydrogen bonds: D:Q.35, D:Q.140 Salt bridges: D:R.52, D:R.52, D:K.139, D:R.149 Metal complexes: D:H.18 HEC.14: 28 residues within 4Å: Chain G: E.276, K.282 Chain H: Y.26, C.27, C.30, H.31, F.80, A.82, A.83, P.84, P.85, L.87, V.90, R.94, W.98, L.99, Y.102, L.103, F.121, V.124, G.125, M.126, P.127, V.129, L.130, L.191 Chain I: G.112, C.113 18 PLIP interactions: 17 interactions with chain H, 1 interactions with chain G, Hydrophobic interactions: H:F.80, H:F.80, H:A.82, H:P.84, H:P.85, H:L.87, H:W.98, H:L.99, H:Y.102, H:L.103, H:V.124, H:P.127, H:V.129, H:L.130 Hydrogen bonds: H:G.125 Salt bridges: H:R.94, G:K.282 Metal complexes: H:H.31 HEC.15: 28 residues within 4Å: Chain H: M.71, W.79 Chain I: Q.35, Y.39, K.42, Q.43, M.107, P.108, A.109, C.110, C.113, H.114, F.126, P.127, L.129, Y.136, V.137, Q.140, L.141, F.144, R.149, N.151, D.152, I.157, M.158, I.161, I.173 Ligands: HEC.16 21 PLIP interactions: 20 interactions with chain I, 1 interactions with chain H, Hydrophobic interactions: I:Y.39, I:P.108, I:F.126, I:L.129, I:L.129, I:V.137, I:F.144, I:D.152, I:I.157, I:I.161, I:I.161, H:W.79 Hydrogen bonds: I:Y.39, I:Q.43, I:Y.136, I:N.151 Salt bridges: I:K.42, I:R.52, I:R.149, I:R.149 Metal complexes: I:H.114 HEC.16: 23 residues within 4Å: Chain I: V.13, C.14, C.17, H.18, F.29, P.30, L.32, Y.39, L.40, Q.43, M.44, R.52, V.54, E.56, M.57, L.60, L.61, L.64, I.72, Y.136, K.139, Q.140 Ligands: HEC.15 22 PLIP interactions: 22 interactions with chain I, Hydrophobic interactions: I:F.29, I:F.29, I:P.30, I:L.32, I:L.40, I:Q.43, I:V.54, I:E.56, I:E.56, I:L.60, I:L.64, I:I.72, I:Y.136 Hydrogen bonds: I:Y.39, I:Q.132, I:Y.136, I:Q.140 Salt bridges: I:R.52, I:R.52, I:K.139, I:R.149 Metal complexes: I:H.18 HEC.22: 25 residues within 4Å: Chain K: F.47, G.48, L.421 Chain L: E.63, G.64, C.65, C.68, H.69, T.105, G.106, P.107, L.109, Y.116, W.120, H.121, H.124, L.125, V.132, S.135, K.136, M.137, P.138, Y.140, L.192 Chain M: I.154 16 PLIP interactions: 14 interactions with chain L, 2 interactions with chain K, Hydrophobic interactions: L:E.63, L:P.107, L:L.109, L:L.109, L:W.120, L:L.125, L:P.138, L:Y.140, L:L.192, K:F.47, K:L.421 Hydrogen bonds: L:Y.116, L:S.135 Salt bridges: L:H.124 pi-Stacking: L:H.124 Metal complexes: L:H.69 HEC.23: 23 residues within 4Å: Chain L: Y.116, S.117 Chain M: C.152, C.155, H.156, G.165, F.166, P.167, L.169, W.174, R.175, W.176, I.183, T.186, I.187, A.193, V.287, M.288, P.289, Q.291, L.303, V.307 Ligands: HEC.24 18 PLIP interactions: 17 interactions with chain M, 1 interactions with chain L, Hydrophobic interactions: M:P.167, M:L.169, M:L.169, M:W.174, M:I.183, M:T.186, M:I.187, M:I.187, M:M.288, M:P.289, M:Q.291, M:L.303, M:L.303, M:V.307, L:Y.116 Hydrogen bonds: M:R.175, M:W.176 Metal complexes: M:H.156 HEC.24: 25 residues within 4Å: Chain M: R.175, A.193, M.195, P.196, W.198, V.210, T.241, C.242, C.245, H.246, M.256, G.257, A.258, P.259, L.261, A.266, F.267, I.268, Y.269, G.270, L.276, T.279, I.280, G.286 Ligands: HEC.23 18 PLIP interactions: 18 interactions with chain M, Hydrophobic interactions: M:A.193, M:P.196, M:W.198, M:P.259, M:L.261, M:Y.269, M:Y.269, M:L.276, M:T.279, M:I.280, M:I.280 Hydrogen bonds: M:I.268, M:Y.269, M:G.270, M:G.286 Salt bridges: M:R.175, M:R.175 Metal complexes: M:H.246

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

CU.17: 4 residues within 4Å: Chain K: H.201, H.251, H.252 Ligands: HEM.21 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:H.251, K:H.252

2 x CA: CALCIUM ION(Non-covalent)

CA.18: 4 residues within 4Å: Chain K: E.116 Chain L: V.66, G.101, S.102 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:E.116 CA.19: 5 residues within 4Å: Chain K: R.51, E.116 Chain L: S.102 Ligands: HEM.20, HEM.21 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain K Metal complexes: L:S.102, K:E.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Di Trani, J.M. et al., Structure of the bc 1 - cbb 3 respiratory supercomplex from Pseudomonas aeruginosa. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-10-11

Peptides

Ubiquinol-cytochrome c reductase iron-sulfur subunit: AF
Cytochrome b: BG
Cytochrome c1: CH
Cytochrome c4: DI
Cytochrome C5: EJ
cytochrome-c oxidase: K
Cbb3-type Cytochrome C oxidase subunit II: L
Cbb3-type cytochrome c oxidase subunit: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

F
Z

B
I

G
D

C
J

H
M

D
K

I
N

E
L

J
O

K
E

L
F

M
G

Membrane

We predict this structure to be a membrane protein.
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Ubiquinol-cytochrome c reductase iron-sulfur subunit

Cytochrome b

Cytochrome c1

Cytochrome c4

Cytochrome C5

cytochrome-c oxidase

Cbb3-type Cytochrome C oxidase subunit II

Cbb3-type cytochrome c oxidase subunit

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