SMTL ID : 7tlj.1

Rhodobacter sphaeroides Mitochondrial respiratory chain complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-mer

Ligands

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

HEM.1: 31 residues within 4Å: Chain A: L.55, Q.58, I.59, G.62, I.63, L.65, A.66, Y.69, V.80, I.83, R.94, H.97, A.98, A.101, F.104, F.105, M.139, T.142, A.143, G.146, Y.147, L.149, P.150, F.195, H.198, Y.199, P.202, F.203, I.205, N.279, Y.297 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:Q.58, A:I.63, A:Y.69, A:A.101, A:F.104, A:T.142, A:L.149, A:L.149, A:Y.199, A:Y.199, A:I.205 Hydrogen bonds: A:N.279 Salt bridges: A:R.94, A:R.94 pi-Stacking: A:H.97, A:H.198 Metal complexes: A:H.97, A:H.198 HEM.2: 31 residues within 4Å: Chain A: W.45, G.48, V.49, L.51, A.52, L.55, F.104, V.108, H.111, I.112, R.114, G.115, S.120, Y.121, R.125, T.128, W.129, G.132, M.133, I.135, Y.136, M.139, I.205, V.209, H.212, I.213, F.216, T.219, G.220, N.221, N.222 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:L.51, A:L.51, A:F.104, A:V.108, A:I.112, A:T.128, A:W.129, A:W.129, A:I.135, A:Y.136, A:V.209, A:V.209, A:F.216, A:F.216, A:F.216 Hydrogen bonds: A:G.48, A:F.216, A:N.222 Salt bridges: A:H.111, A:R.114, A:R.125 Metal complexes: A:H.111, A:H.212 HEM.7: 31 residues within 4Å: Chain E: L.55, Q.58, I.59, G.62, I.63, L.65, A.66, Y.69, V.80, I.83, R.94, H.97, A.98, A.101, F.104, F.105, M.139, T.142, A.143, G.146, Y.147, L.149, P.150, F.195, H.198, Y.199, P.202, F.203, I.205, N.279, Y.297 19 PLIP interactions: 19 interactions with chain E, Hydrophobic interactions: E:Q.58, E:I.63, E:Y.69, E:A.101, E:F.104, E:T.142, E:L.149, E:L.149, E:Y.199, E:Y.199, E:I.205 Hydrogen bonds: E:N.279 Salt bridges: E:R.94, E:R.94 pi-Stacking: E:H.97, E:H.198, E:H.198 Metal complexes: E:H.97, E:H.198 HEM.8: 31 residues within 4Å: Chain E: W.45, G.48, V.49, L.51, A.52, L.55, F.104, V.108, H.111, I.112, R.114, G.115, S.120, Y.121, R.125, T.128, W.129, G.132, M.133, I.135, Y.136, M.139, I.205, V.209, H.212, I.213, F.216, T.219, G.220, N.221, N.222 19 PLIP interactions: 19 interactions with chain E, Hydrophobic interactions: E:L.51, E:L.51, E:F.104, E:I.112, E:I.135, E:Y.136, E:V.209, E:F.216, E:F.216, E:F.216 Hydrogen bonds: E:G.48, E:N.222 Salt bridges: E:H.111, E:R.114, E:R.125 pi-Stacking: E:H.212 pi-Cation interactions: E:R.114 Metal complexes: E:H.111, E:H.212

2 x PQU: (5S)-3-anilino-5-methyl-5-(6-phenoxypyridin-3-yl)-1,3-oxazolidine-2,4-dione(Non-covalent)

PQU.3: 22 residues within 4Å: Chain A: M.140, A.141, A.143, F.144, Y.147, V.148, M.154, G.158, A.159, V.161, I.162, L.165, F.166, I.292, V.293, P.294, E.295, Y.297, F.298, Y.302, M.336, F.337 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.144, A:Y.147, A:V.161, A:I.162, A:I.162, A:F.166, A:I.292, A:P.294, A:P.294, A:E.295, A:F.298, A:F.298, A:F.298, A:Y.302, A:F.337 Hydrogen bonds: A:E.295 pi-Stacking: A:F.298 PQU.9: 20 residues within 4Å: Chain E: M.140, A.141, A.143, F.144, Y.147, V.148, S.155, G.158, V.161, I.162, F.166, I.292, V.293, P.294, E.295, Y.297, F.298, Y.302, M.336, F.337 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:F.144, E:Y.147, E:V.161, E:I.162, E:I.162, E:F.166, E:I.292, E:P.294, E:P.294, E:E.295, E:F.298, E:F.298, E:F.298, E:Y.302 Hydrogen bonds: E:E.295 pi-Stacking: E:F.298

2 x LOP: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE(Non-covalent)

LOP.4: 19 residues within 4Å: Chain A: N.42, M.44, I.106, Y.109, L.110, F.113, R.114, Y.117, Y.118, P.224, Y.273, L.274, W.296, R.358, F.367, W.368, A.371, F.374, V.375 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.106, A:I.106, A:Y.109, A:F.113, A:F.113, A:F.113, A:F.367, A:A.371, A:F.374 Hydrogen bonds: A:R.358 Salt bridges: A:R.358 LOP.10: 19 residues within 4Å: Chain E: M.44, I.106, Y.109, L.110, F.113, R.114, Y.117, Y.118, Y.273, W.296, R.358, F.367, W.368, A.371, F.374, V.375 Chain F: T.116, I.118, L.121 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:I.106, E:Y.109, E:L.110, E:F.113, E:Y.117, E:W.368, E:A.371, E:F.374 Hydrogen bonds: E:Y.117, E:Y.118 Salt bridges: E:R.358

2 x HEC: HEME C(Covalent)

HEC.5: 26 residues within 4Å: Chain B: V.31, V.35, C.36, A.38, C.39, H.40, L.94, N.96, A.97, P.98, L.100, M.103, R.107, Y.130, I.131, V.134, L.135, F.160, I.183, A.184, M.185, P.186, P.188, L.189, V.211, L.215 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:V.35, B:L.94, B:A.97, B:L.100, B:L.135, B:I.183, B:A.184, B:P.188, B:L.189, B:V.211 Hydrogen bonds: B:Y.130, B:Y.130, B:A.184 Salt bridges: B:R.107 Metal complexes: B:H.40 HEC.11: 27 residues within 4Å: Chain F: V.31, V.35, C.36, A.38, C.39, H.40, L.94, N.96, A.97, P.98, L.100, M.103, R.107, Y.130, I.131, V.134, L.135, F.160, N.162, I.183, A.184, M.185, P.186, P.188, L.189, V.211, L.215 10 PLIP interactions: 10 interactions with chain F, Hydrophobic interactions: F:P.98, F:L.135, F:I.183, F:P.188, F:V.211, F:L.215 Hydrogen bonds: F:Y.130, F:A.184 Salt bridges: F:R.107 Metal complexes: F:H.40

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

FES.6: 10 residues within 4Å: Chain C: C.129, H.131, L.132, G.133, C.134, C.149, C.151, H.152, S.154, P.166 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.129, C:H.131, C:C.149, C:H.152 FES.12: 12 residues within 4Å: Chain G: C.129, H.131, L.132, G.133, C.134, C.149, C.151, H.152, G.153, S.154, P.166, A.167 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.129, G:H.131, G:C.149, G:H.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, D. et al., Conformation Switch of Rieske ISP subunit is revealed by the Crystal Structure of Bacterial Cytochrome bc1 in Complex with Azoxystrobin. to be published

Release Date

2023-02-08

Peptides

Cytochrome b: AE
Cytochrome c1: BF
Ubiquinol-cytochrome c reductase iron-sulfur subunit: CG
14 kDa peptide of ubiquinol-cytochrome c2 oxidoreductase complex: 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 b

Cytochrome c1

Ubiquinol-cytochrome c reductase iron-sulfur subunit

14 kDa peptide of ubiquinol-cytochrome c2 oxidoreductase complex

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