- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-2-2-2-2-mer
- Ligands
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 12 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)
PEE.2: 6 residues within 4Å:- Chain A: W.32, I.35, N.39
- Chain F: S.175, W.179
- Ligands: U10.16
5 PLIP interactions:4 interactions with chain F, 1 interactions with chain A- Hydrophobic interactions: F:W.179, F:W.179, F:W.179
- Hydrogen bonds: F:S.175, A:N.39
PEE.3: 19 residues within 4Å:- Chain A: R.12, D.13, Y.16, Y.17, T.19, A.20, G.21, A.22, A.24, V.25
- Chain B: W.245, P.246, I.250
- Chain C: L.273
- Chain D: F.88, G.91, A.92, A.95
- Ligands: PEE.10
17 PLIP interactions:1 interactions with chain B, 10 interactions with chain A, 6 interactions with chain D- Hydrophobic interactions: B:P.246, A:Y.16, A:Y.17, A:Y.17, A:T.19, A:A.20, A:A.24, A:V.25, A:V.25, D:F.88, D:F.88, D:F.88, D:A.92, D:A.95
- Hydrogen bonds: A:Y.17
- Salt bridges: A:R.12, D:R.84
PEE.6: 12 residues within 4Å:- Chain B: M.1, L.28, D.31, T.32, V.209, A.210, I.213, W.214, H.217
- Chain F: L.28
- Ligands: PEE.10, PEE.17
11 PLIP interactions:10 interactions with chain B, 1 interactions with chain F- Hydrophobic interactions: B:T.32, B:V.209, B:A.210, B:I.213, B:I.213, B:W.214, F:L.28
- Hydrogen bonds: B:M.1, B:M.1, B:D.31
- Salt bridges: B:H.217
PEE.7: 12 residues within 4Å:- Chain A: A.29, A.30, P.33
- Chain B: L.57, N.88, G.89, F.91, M.92, L.96
- Chain C: T.254, A.255, F.258
7 PLIP interactions:1 interactions with chain A, 2 interactions with chain C, 4 interactions with chain B- Hydrophobic interactions: A:P.33, C:A.255, C:F.258, B:L.57, B:L.96
- Hydrogen bonds: B:N.88, B:G.89
PEE.8: 9 residues within 4Å:- Chain B: M.44, L.110, F.113, Y.117, Y.118, R.358, F.367, W.368, A.371
12 PLIP interactions:12 interactions with chain B- Hydrophobic interactions: B:L.110, B:F.113, B:F.113, B:Y.117, B:Y.117, B:Y.118, B:F.367, B:A.371
- Hydrogen bonds: B:Y.117, B:Y.117, B:Y.118
- Salt bridges: B:R.358
PEE.9: 5 residues within 4Å:- Chain B: S.175, W.179
- Chain E: W.32, I.35, N.39
7 PLIP interactions:2 interactions with chain E, 5 interactions with chain B- Hydrophobic interactions: E:W.32, E:I.35, B:W.179, B:W.179, B:W.179, B:W.179, B:W.179
PEE.10: 12 residues within 4Å:- Chain B: Y.9, R.12, L.28, A.29, Y.30, T.32, I.33, M.34, W.245
- Ligands: PEE.3, HEM.4, PEE.6
8 PLIP interactions:8 interactions with chain B- Hydrophobic interactions: B:L.28, B:A.29, B:T.32, B:I.33, B:W.245
- Hydrogen bonds: B:R.12, B:Y.30
- Salt bridges: B:R.12
PEE.13: 16 residues within 4Å:- Chain E: A.26, A.29, A.30, P.33, L.34
- Chain F: L.57, N.88, G.89, M.92, L.96
- Chain G: K.244, A.251, T.254, A.255, F.258, L.259
10 PLIP interactions:5 interactions with chain G, 2 interactions with chain E, 3 interactions with chain F- Hydrophobic interactions: G:A.255, G:F.258, G:L.259, E:P.33, E:L.34, F:L.57, F:M.92
- Hydrogen bonds: G:K.244, G:K.244, F:G.89
PEE.17: 9 residues within 4Å:- Chain B: P.24
- Chain F: M.1, L.28, T.32, A.210, I.213, W.214, H.217
- Ligands: PEE.6
6 PLIP interactions:6 interactions with chain F- Hydrophobic interactions: F:L.28, F:T.32, F:W.214, F:W.214, F:H.217
- Hydrogen bonds: F:M.1
PEE.18: 6 residues within 4Å:- Chain F: E.16, A.29, Y.30, I.33, M.34, W.245
4 PLIP interactions:4 interactions with chain F- Hydrophobic interactions: F:A.29, F:W.245
- Hydrogen bonds: F:E.16, F:W.245
PEE.19: 9 residues within 4Å:- Chain F: L.345, W.348, L.349, T.351, A.398, F.401, A.402, L.405, P.409
4 PLIP interactions:4 interactions with chain F- Hydrophobic interactions: F:L.345, F:A.398, F:F.401, F:A.402
PEE.20: 9 residues within 4Å:- Chain B: G.14, I.15, W.18
- Chain F: I.130, L.137, I.211, A.344, L.345, W.348
7 PLIP interactions:6 interactions with chain F, 1 interactions with chain B- Hydrophobic interactions: F:I.130, F:L.137, F:I.211, F:A.344, F:W.348, F:W.348, B:W.18
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
HEM.4: 24 residues within 4Å:- Chain B: W.45, G.48, L.51, A.52, F.104, H.111, I.112, R.114, S.120, R.125, T.128, W.129, G.132, M.133, I.135, Y.136, V.209, H.212, F.216, T.219, G.220, N.221, N.222
- Ligands: PEE.10
20 PLIP interactions:20 interactions with chain B,- Hydrophobic interactions: B:L.51, B:L.51, B:F.104, B:I.112, B:I.112, B:W.129, B:W.129, B:I.135, B:Y.136, B:V.209, B:F.216
- Hydrogen bonds: B:G.48, B:T.219, B:T.219, B:N.222
- Salt bridges: B:H.111, B:R.114, B:R.125
- pi-Stacking: B:H.212
- Metal complexes: B:H.111
HEM.5: 23 residues within 4Å:- Chain B: Q.58, I.59, G.62, I.63, L.65, A.66, Y.69, R.94, H.97, A.98, A.101, F.104, T.142, A.143, G.146, Y.147, L.149, P.150, H.198, Y.199, P.202, I.205, Y.297
16 PLIP interactions:16 interactions with chain B,- Hydrophobic interactions: B:Q.58, B:A.66, B:Y.69, B:A.98, B:A.101, B:F.104, B:T.142, B:L.149, B:L.149, B:Y.199, B:P.202, B:I.205
- Salt bridges: B:R.94, B:R.94
- Metal complexes: B:H.97, B:H.198
HEM.14: 22 residues within 4Å:- Chain F: W.45, G.48, L.51, A.52, F.104, H.111, I.112, R.114, S.120, R.125, W.129, G.132, M.133, I.135, Y.136, V.209, H.212, F.216, T.219, G.220, N.221, N.222
20 PLIP interactions:20 interactions with chain F,- Hydrophobic interactions: F:L.51, F:L.51, F:F.104, F:I.112, F:W.129, F:W.129, F:I.135, F:Y.136, F:V.209, F:F.216, F:F.216
- Hydrogen bonds: F:G.48, F:T.219, F:T.219, F:N.222
- Salt bridges: F:H.111, F:R.114, F:R.125
- Metal complexes: F:H.111, F:H.212
HEM.15: 21 residues within 4Å:- Chain F: Q.58, G.62, I.63, L.65, Y.69, R.94, H.97, A.98, A.101, F.104, T.142, A.143, G.146, Y.147, L.149, P.150, H.198, Y.199, P.202, I.205, Y.297
16 PLIP interactions:16 interactions with chain F,- Hydrophobic interactions: F:Q.58, F:I.63, F:Y.69, F:A.101, F:F.104, F:T.142, F:L.149, F:L.149, F:Y.199, F:Y.199, F:P.202, F:I.205
- Salt bridges: F:R.94, F:R.94
- Metal complexes: F:H.97, F:H.198
- 2 x HEC: HEME C(Covalent)
HEC.11: 17 residues within 4Å:- Chain C: V.57, C.58, C.61, H.62, L.116, N.118, P.120, M.125, R.129, Y.152, L.157, F.182, I.205, A.206, M.207, V.233, L.237
12 PLIP interactions:12 interactions with chain C,- Hydrophobic interactions: C:V.57, C:L.116, C:Y.152, C:L.157, C:L.157, C:A.206, C:V.233, C:L.237
- Hydrogen bonds: C:Y.152, C:A.206
- Salt bridges: C:R.129
- Metal complexes: C:H.62
HEC.21: 19 residues within 4Å:- Chain G: V.57, C.58, C.61, H.62, L.116, N.118, A.119, P.120, L.122, M.125, R.129, Y.152, L.157, F.182, I.205, A.206, M.207, P.208, P.210
11 PLIP interactions:11 interactions with chain G,- Hydrophobic interactions: G:V.57, G:N.118, G:A.119, G:Y.152, G:L.157, G:I.205, G:A.206
- Hydrogen bonds: G:N.184, G:A.206
- Salt bridges: G:R.129
- Metal complexes: G:H.62
- 1 x U10: UBIQUINONE-10(Non-covalent)
U10.16: 25 residues within 4Å:- Chain A: L.34, I.35, M.38, H.152
- Chain B: I.63, V.64, M.67
- Chain F: M.140, A.141, F.144, M.145, G.158, V.161, I.162, W.179, L.180, F.194, L.197, I.292, P.294, F.298, F.301, Y.302, L.305
- Ligands: PEE.2
20 PLIP interactions:2 interactions with chain B, 17 interactions with chain F, 1 interactions with chain A- Hydrophobic interactions: B:I.63, B:V.64, F:M.140, F:F.144, F:F.144, F:I.162, F:W.179, F:W.179, F:L.180, F:F.194, F:L.197, F:P.294, F:P.294, F:F.298, F:F.298, F:F.298, F:F.301, F:Y.302, F:Y.302, A:I.35
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Swainsbury, D.J.K. et al., Cryo-EM structure of the four-subunit Rhodobacter sphaeroides cytochrome bc 1 complex in styrene maleic acid nanodiscs. Proc.Natl.Acad.Sci.USA (2023)
- Release Date
- 2023-03-15
- Peptides
- Ubiquinol-cytochrome c reductase iron-sulfur subunit: AE
Cytochrome b: BF
Cytochrome c1: CG
Cytochrome b-c1 subunit IV: DH - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AE
EB
BF
FC
CG
GD
DH
H - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-2-2-2-2-mer
- Ligands
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 12 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 2 x HEC: HEME C(Covalent)
- 1 x U10: UBIQUINONE-10(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Swainsbury, D.J.K. et al., Cryo-EM structure of the four-subunit Rhodobacter sphaeroides cytochrome bc 1 complex in styrene maleic acid nanodiscs. Proc.Natl.Acad.Sci.USA (2023)
- Release Date
- 2023-03-15
- Peptides
- Ubiquinol-cytochrome c reductase iron-sulfur subunit: AE
Cytochrome b: BF
Cytochrome c1: CG
Cytochrome b-c1 subunit IV: DH - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AE
EB
BF
FC
CG
GD
DH
H - Membrane
-
We predict this structure to be a membrane protein.