SMTL ID : 8snh.1

cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.201, H.251, H.252 Ligands: HEM.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.251, A:H.252

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: E.116 Chain L: V.66, G.101, S.102 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.116 CA.3: 6 residues within 4Å: Chain A: R.51, E.116 Chain L: S.102, K.103 Ligands: HEM.4, HEM.5 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain A Metal complexes: L:S.102, A:E.116

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

HEM.4: 34 residues within 4Å: Chain A: M.23, G.26, V.27, I.29, A.30, L.33, F.47, R.51, H.54, T.55, V.58, I.59, F.62, E.116, Y.117, L.208, D.334, T.336, I.337, V.340, H.341, A.344, L.345, V.348, A.349, Y.389, R.431, G.435, F.438, L.439 Chain L: K.103, T.105 Ligands: CA.3, HEM.5 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain L, Hydrophobic interactions: A:I.29, A:A.30, A:T.55, A:V.58, A:V.58, A:Y.117, A:I.337, A:I.337, A:V.340, A:V.340, A:A.344, A:V.348, A:Y.389, A:F.438 Hydrogen bonds: A:Y.117, A:D.334 Salt bridges: A:R.51, A:R.51, A:R.431, L:K.103 pi-Stacking: A:Y.389 Metal complexes: A:H.54 HEM.5: 31 residues within 4Å: Chain A: E.116, Y.117, W.197, V.204, L.208, T.209, Y.245, H.251, H.252, S.270, L.273, S.277, S.314, T.315, G.318, P.319, M.321, A.322, N.327, H.331, T.336, H.339, V.340, G.343, A.344, W.347, V.348 Chain L: S.102 Ligands: CU.1, CA.3, HEM.4 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:V.204, A:L.208, A:L.273, A:T.315, A:M.321, A:T.336, A:V.340, A:V.340, A:V.348 Hydrogen bonds: A:H.252, A:N.327, A:T.336 Salt bridges: A:H.331 pi-Cation interactions: A:H.201, A:H.252 Metal complexes: A:H.339 HEM.8: 31 residues within 4Å: Chain C: Y.35, F.37, G.38, S.39, A.41, L.42, L.45, F.94, V.98, H.101, M.102, R.104, G.105, S.110, Y.111, R.115, V.118, W.119, G.122, M.123, I.125, Y.126, L.129, L.196, V.200, H.203, I.204, L.207, S.212, N.213, F.236 23 PLIP interactions: 23 interactions with chain C, Hydrophobic interactions: C:A.41, C:L.42, C:L.42, C:F.94, C:V.98, C:V.98, C:V.118, C:W.119, C:W.119, C:I.125, C:Y.126, C:L.129, C:L.207, C:L.207 Hydrogen bonds: C:Y.35, C:G.38, C:S.110, C:N.213 Salt bridges: C:H.101, C:R.104, C:R.104 pi-Cation interactions: C:R.104 Metal complexes: C:H.203 HEM.9: 32 residues within 4Å: Chain C: L.45, Q.48, I.49, G.52, I.53, L.55, T.56, F.59, V.70, I.73, R.84, H.87, S.88, A.91, F.94, F.95, L.129, E.132, A.133, G.136, Y.137, L.139, P.140, F.185, H.188, V.189, P.193, L.196, L.270, N.274, Y.292 Chain H: I.190 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain H, Hydrophobic interactions: C:Q.48, C:I.53, C:L.55, C:F.59, C:F.59, C:F.94, C:L.129, C:E.132, C:L.139, C:L.139, C:P.140, C:V.189, C:V.189, C:P.193, C:L.196, H:I.190 Hydrogen bonds: C:N.274 Salt bridges: C:R.84, C:R.84 Metal complexes: C:H.87, C:H.188 HEM.16: 30 residues within 4Å: Chain H: Y.35, F.37, G.38, S.39, A.41, L.42, L.45, F.94, V.98, H.101, M.102, R.104, G.105, S.110, Y.111, R.115, V.118, W.119, G.122, M.123, I.125, Y.126, L.129, V.200, H.203, I.204, L.207, S.212, N.213, F.236 24 PLIP interactions: 24 interactions with chain H, Hydrophobic interactions: H:A.41, H:L.42, H:F.94, H:V.98, H:V.98, H:V.118, H:W.119, H:W.119, H:W.119, H:I.125, H:Y.126, H:L.129, H:L.207, H:L.207 Hydrogen bonds: H:Y.35, H:G.38, H:S.39, H:S.110, H:N.213 Salt bridges: H:H.101, H:R.104, H:R.104 pi-Cation interactions: H:R.104 Metal complexes: H:H.203 HEM.17: 31 residues within 4Å: Chain C: I.190 Chain H: L.45, Q.48, I.49, G.52, I.53, L.55, T.56, F.59, V.70, I.73, R.84, H.87, S.88, A.91, F.94, F.95, L.129, E.132, A.133, G.136, Y.137, L.139, P.140, F.185, H.188, V.189, P.193, L.196, L.270, Y.292 19 PLIP interactions: 18 interactions with chain H, 1 interactions with chain C, Hydrophobic interactions: H:Q.48, H:I.53, H:L.55, H:F.59, H:F.59, H:F.94, H:L.129, H:E.132, H:L.139, H:L.139, H:V.189, H:V.189, H:P.193, H:L.196, C:I.190 Salt bridges: H:R.84, H:R.84 Metal complexes: H:H.87, H:H.188

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

FES.6: 10 residues within 4Å: Chain B: C.122, H.124, L.125, C.127, C.150, C.152, H.153, S.155, Y.157, P.168 6 PLIP interactions: 6 interactions with chain B, Metal complexes: B:C.122, B:H.124, B:H.124, B:C.127, B:C.150, B:H.153 FES.14: 10 residues within 4Å: Chain G: C.122, H.124, L.125, C.127, C.150, C.152, H.153, S.155, P.168 Chain H: V.151 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.122, G:H.124, G:C.150, G:H.153

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.7: 12 residues within 4Å: Chain C: A.302, V.303, P.304, M.308, V.311, A.312, A.315, R.372, T.375, V.376, F.379, I.383 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:A.302, C:V.303, C:A.312, C:A.315, C:T.375, C:F.379, C:F.379, C:F.379, C:F.379, C:I.383 I7Y.15: 19 residues within 4Å: Chain G: Q.89, D.143, H.156, Y.164, K.165, G.166, Q.167 Chain H: 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: 4 interactions with chain G, 9 interactions with chain H Hydrogen bonds: G:D.143, G:K.165, G:G.166, G:Q.167 Hydrophobic interactions: H:V.303, H:A.312, H:A.315, H:R.372, H:T.375, H:F.379, H:F.379, H:F.379, H:I.383

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

U10.10: 42 residues within 4Å: Chain B: G.20, G.23, A.24, A.27, A.28, F.31, V.32, W.35 Chain C: M.130, A.131, F.134, M.135, G.148, V.151, I.152, I.153, L.155, F.156, L.166, W.169, I.170, F.184, L.187, I.287, A.288, P.289, V.290, F.293, F.296, Y.297, L.300, M.313, I.317 Chain H: L.43, V.46, L.50, W.54, I.245, V.248, V.249, L.252 Chain I: F.220 17 PLIP interactions: 3 interactions with chain H, 9 interactions with chain C, 4 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: H:W.54, H:V.248, H:L.252, C:F.134, C:L.155, C:F.156, C:I.170, C:F.293, C:F.296, C:Y.297, C:L.300, B:A.27, B:F.31, B:V.32, B:W.35, I:F.220 pi-Stacking: C:Y.297 U10.18: 45 residues within 4Å: Chain C: L.43, V.46, L.50, W.54, I.245, V.248, L.252 Chain D: F.220 Chain G: G.20, G.23, A.24, A.27, A.28, F.31, V.32, W.35, L.125, C.152, H.153 Chain H: M.130, A.131, F.134, M.135, M.144, G.148, V.151, I.152, I.153, L.155, F.156, L.166, W.169, I.170, F.184, L.187, I.287, A.288, P.289, V.290, F.293, F.296, Y.297, L.300, M.313, I.317 18 PLIP interactions: 5 interactions with chain C, 8 interactions with chain H, 4 interactions with chain G, 1 interactions with chain D Hydrophobic interactions: C:L.43, C:L.50, C:W.54, C:V.248, C:L.252, H:F.134, H:V.151, H:I.152, H:F.156, H:I.170, H:Y.297, H:Y.297, H:L.300, G:A.27, G:W.35, G:W.35, D:F.220 Hydrogen bonds: G:H.153

9 x HEC: HEME C(Covalent)

HEC.11: 33 residues within 4Å: Chain C: E.276 Chain D: F.23, Y.26, C.27, G.29, C.30, H.31, F.80, A.82, A.83, P.84, P.85, L.87, V.90, V.93, 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, L.195 Chain E: G.112, C.113, I.121, F.126 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:Y.26, D:F.80, D:F.80, D:A.82, D:P.84, D:P.85, D:W.98, D:W.98, D:L.99, D:Y.102, D:L.103, D:V.124, D:M.126, D:V.129, D:L.130 Hydrogen bonds: D:G.125 Salt bridges: D:R.94 Metal complexes: D:H.31 HEC.12: 36 residues within 4Å: Chain D: M.71, W.79, F.80 Chain E: Q.35, Y.39, K.42, Q.43, R.52, F.98, M.107, P.108, A.109, C.110, G.112, C.113, H.114, G.125, F.126, P.127, L.129, Q.132, 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, I.177 Ligands: HEC.13 25 PLIP interactions: 24 interactions with chain E, 1 interactions with chain D, Hydrophobic interactions: E:Y.39, E:P.108, E:F.126, E:F.126, E:L.129, E:L.129, E:V.137, E:F.144, E:D.152, E:I.157, E:I.157, E:I.161, E:I.161, D:F.80 Hydrogen bonds: E:Q.35, E:Y.39, E:Q.43, E:Q.132, E:Y.136, E:N.151 Salt bridges: E:K.42, E:R.52, E:R.149, E:R.149 Metal complexes: E:H.114 HEC.13: 31 residues within 4Å: Chain E: V.13, C.14, A.16, C.17, H.18, N.28, F.29, P.30, L.32, Q.35, Y.39, L.40, Q.43, M.44, I.47, R.52, V.54, E.56, M.57, L.60, L.61, L.64, L.69, I.72, F.76, Q.132, Y.136, K.139, Q.140, R.149 Ligands: HEC.12 21 PLIP interactions: 21 interactions with chain E, Hydrophobic interactions: E:F.29, E:F.29, E:P.30, E:L.32, E:L.40, E:Q.43, E:V.54, E:E.56, E:E.56, E:L.60, E:L.64, E:I.72, E:Y.136 Hydrogen bonds: E:Y.39, E:Y.136, E:Q.140 Salt bridges: E:R.52, E:R.52, E:K.139, E:R.149 Metal complexes: E:H.18 HEC.19: 35 residues within 4Å: Chain H: E.276, K.282 Chain I: T.22, F.23, Y.26, C.27, G.29, C.30, H.31, F.80, A.82, A.83, P.84, P.85, L.87, V.90, V.93, 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, L.195 Chain J: G.112, C.113, I.121, F.126 21 PLIP interactions: 20 interactions with chain I, 1 interactions with chain H, Hydrophobic interactions: I:F.80, I:F.80, I:F.80, I:A.82, I:P.84, I:P.85, I:L.87, I:L.87, I:W.98, I:L.99, I:Y.102, I:L.103, I:V.124, I:P.127, I:V.129, I:L.130 Hydrogen bonds: I:G.125 Salt bridges: I:R.94, H:K.282 pi-Cation interactions: I:H.31 Metal complexes: I:H.31 HEC.20: 35 residues within 4Å: Chain I: M.71, W.79, F.80 Chain J: Q.35, Y.39, K.42, Q.43, R.52, F.98, M.107, P.108, A.109, C.110, C.113, H.114, G.125, F.126, P.127, L.129, Q.132, 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, I.177 Ligands: HEC.21 22 PLIP interactions: 21 interactions with chain J, 1 interactions with chain I, Hydrophobic interactions: J:Y.39, J:P.108, J:F.126, J:L.129, J:L.129, J:V.137, J:F.144, J:D.152, J:I.157, J:I.161, J:I.161, I:W.79 Hydrogen bonds: J:Q.35, J:Y.39, J:Q.43, J:Y.136, J:N.151 Salt bridges: J:K.42, J:R.52, J:R.149, J:R.149 Metal complexes: J:H.114 HEC.21: 30 residues within 4Å: Chain J: V.13, C.14, A.16, C.17, H.18, N.28, F.29, P.30, L.32, Q.35, Y.39, L.40, Q.43, M.44, I.47, R.52, V.54, E.56, M.57, L.60, L.61, L.64, I.72, F.76, Q.132, Y.136, K.139, Q.140, R.149 Ligands: HEC.20 22 PLIP interactions: 22 interactions with chain J, Hydrophobic interactions: J:F.29, J:F.29, J:P.30, J:L.32, J:L.40, J:Q.43, J:V.54, J:E.56, J:E.56, J:L.60, J:L.64, J:I.72, J:Y.136 Hydrogen bonds: J:Y.39, J:Q.132, J:Y.136, J:Q.140 Salt bridges: J:R.52, J:R.52, J:K.139, J:R.149 Metal complexes: J:H.18 HEC.22: 32 residues within 4Å: Chain A: L.33, F.47, G.48, F.417, V.418, L.421 Chain L: Y.60, E.63, G.64, C.65, C.68, H.69, T.105, G.106, P.107, L.109, V.112, Y.116, W.120, H.121, H.124, L.125, P.128, V.132, S.135, K.136, M.137, P.138, Y.140, L.143, L.192 Chain M: I.145 17 PLIP interactions: 2 interactions with chain A, 15 interactions with chain L, Hydrophobic interactions: A:F.47, A:L.421, L:E.63, L:P.107, L:L.109, L:W.120, L:W.120, L:L.125, L:M.137, L:P.138, L:Y.140, L:L.192 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: 35 residues within 4Å: Chain L: R.115, Y.116, S.117, W.120 Chain M: F.139, Y.142, C.143, I.145, C.146, H.147, G.156, F.157, P.158, L.160, E.164, W.165, R.166, W.167, G.168, I.174, T.177, I.178, R.182, A.184, I.259, Y.260, G.277, Q.278, M.279, P.280, Q.282, L.286, L.294, I.298 Ligands: HEC.24 23 PLIP interactions: 22 interactions with chain M, 1 interactions with chain L, Hydrophobic interactions: M:F.157, M:F.157, M:P.158, M:L.160, M:W.165, M:W.165, M:R.166, M:T.177, M:I.178, M:P.280, M:Q.282, M:I.298, L:Y.116 Hydrogen bonds: M:R.166, M:W.167, M:W.167, M:G.168, M:G.168, M:Y.260, M:G.277 Salt bridges: M:R.166 pi-Stacking: M:H.147 Metal complexes: M:H.147 HEC.24: 31 residues within 4Å: Chain M: R.166, A.184, I.185, M.186, A.187, W.189, L.193, V.201, V.205, I.228, F.229, N.232, C.233, A.235, C.236, H.237, V.247, G.248, A.249, P.250, L.252, F.258, I.259, Y.260, L.267, T.270, I.271, R.275, Q.276, G.277 Ligands: HEC.23 18 PLIP interactions: 18 interactions with chain M, Hydrophobic interactions: M:I.185, M:W.189, M:V.201, M:V.201, M:V.205, M:L.252, M:F.258, M:F.258, M:Y.260, M:L.267, M:T.270, M:I.271 Hydrogen bonds: M:I.259, M:Y.260, M:G.277 Salt bridges: M:R.166, M:R.166 Metal complexes: M:H.237

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
C

G
Z

C
I

H
D

D
J

I
M

E
K

J
N

F
L

K
O

L
F

M
G

Membrane

We predict this structure to be a membrane protein.
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cytochrome-c oxidase

Ubiquinol-cytochrome c reductase iron-sulfur subunit

Cytochrome b

Cytochrome c1

Cytochrome c4

Cytochrome C5

Cbb3-type Cytochrome C oxidase subunit II

Cbb3-type cytochrome c oxidase subunit

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