SMTL ID : 6nin.3 (2 other biounits)

Rhodobacter sphaeroides bc1 with STIGMATELLIN A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

HEM.1: 29 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, I.205, V.209, H.212, F.216, T.219, G.220, N.221, N.222 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:L.51, A:L.51, A:L.51, A:A.52, A:F.104, A:V.108, A:I.112, A:I.135, A:V.209, A:F.216, A:F.216, A:F.216, A:F.216 Hydrogen bonds: A:G.48, A:T.219, A:T.219, A:N.222 Salt bridges: A:H.111, A:R.114, A:R.125 Metal complexes: A:H.111, A:H.212 HEM.2: 31 residues within 4Å: Chain A: L.55, Q.58, I.59, G.62, I.63, L.65, A.66, Y.69, V.80, 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 Chain D: S.196 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:L.55, A:Q.58, A:I.59, A:I.63, A:A.98, A:A.101, A:F.104, A:T.142, A:L.149, A:L.149, A:F.195, A:Y.199, A:Y.199 Salt bridges: A:R.94, A:R.94 Metal complexes: A:H.97, A:H.198 HEM.8: 31 residues within 4Å: Chain D: 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 D, Hydrophobic interactions: D:L.51, D:L.51, D:F.104, D:V.108, D:I.112, D:T.128, D:W.129, D:W.129, D:I.135, D:Y.136, D:V.209, D:F.216, D:F.216, D:F.216 Hydrogen bonds: D:G.48, D:T.219, D:T.219, D:N.222 Salt bridges: D:H.111, D:R.114, D:R.125 Metal complexes: D:H.111, D:H.212 HEM.9: 30 residues within 4Å: Chain A: S.196 Chain D: L.55, Q.58, I.59, G.62, I.63, L.65, A.66, Y.69, V.80, R.94, H.97, A.98, A.101, F.104, 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 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:L.55, D:Q.58, D:I.59, D:A.66, D:A.98, D:A.101, D:F.104, D:T.142, D:L.149, D:L.149, D:F.195, D:Y.199 Hydrogen bonds: D:N.279 Salt bridges: D:R.94, D:R.94 Metal complexes: D:H.97, D:H.198

2 x SMA: STIGMATELLIN A(Non-covalent)

SMA.3: 29 residues within 4Å: Chain A: L.137, M.140, A.141, F.144, M.145, Y.147, M.154, G.158, V.161, I.162, T.163, L.165, F.166, L.180, F.194, L.197, I.292, V.293, P.294, E.295, F.298, F.301, Y.302, L.305, M.336, F.337, I.340 Chain F: C.151, H.152 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.144, A:F.144, A:F.144, A:V.161, A:F.166, A:L.180, A:F.194, A:L.197, A:P.294, A:F.298, A:F.301, A:Y.302, A:L.305 Hydrogen bonds: A:E.295 SMA.10: 30 residues within 4Å: Chain C: L.132, C.151, H.152 Chain D: L.137, M.140, A.141, F.144, M.145, Y.147, M.154, G.158, V.161, I.162, T.163, L.165, F.166, L.180, F.194, L.197, I.292, V.293, P.294, E.295, F.298, F.301, Y.302, L.305, M.336, F.337, I.340 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:A.141, D:F.144, D:F.144, D:F.144, D:V.161, D:F.166, D:F.166, D:L.180, D:L.197, D:P.294, D:F.298, D:F.301, D:Y.302 Hydrogen bonds: D:E.295

2 x HEC: HEME C(Covalent)

HEC.4: 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 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:V.35, B:L.94, B:A.97, B:P.98, B:L.135, B:I.183, B:P.188, B:L.189 Hydrogen bonds: B:Y.130, B:Y.130, B:A.184 Salt bridges: B:R.107 Metal complexes: B:H.40 HEC.12: 26 residues within 4Å: Chain E: 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 11 PLIP interactions: 11 interactions with chain E, Hydrophobic interactions: E:V.31, E:V.35, E:P.98, E:I.131, E:L.135, E:I.183 Hydrogen bonds: E:Y.130, E:Y.130, E:A.184 Salt bridges: E:R.107 Metal complexes: E:H.40

2 x SR: STRONTIUM ION(Non-functional Binders)

SR.5: 5 residues within 4Å: Chain B: D.8, V.9, P.10, E.14, E.129 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.8, B:V.9, B:E.14, B:E.14, B:E.129 SR.13: 6 residues within 4Å: Chain E: D.8, V.9, P.10, E.14, F.110, E.129 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.8, E:V.9, E:E.14, E:E.14, E:E.129

2 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.6: 16 residues within 4Å: Chain A: L.261, A.265, F.269, M.270 Chain B: F.13, E.14, G.15, P.16, L.121, F.122, N.123, G.124, I.125, R.226, K.227, V.234 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.15, B:F.122, B:R.226, B:K.227 Hydrophobic interactions: A:A.265, A:F.269 BOG.14: 14 residues within 4Å: Chain D: V.262, A.265, I.266, F.269, M.270 Chain E: F.13, E.14, G.15, P.16, F.122, N.123, G.124, R.226, K.227 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:G.15, E:F.122, E:R.226, E:K.227 Hydrophobic interactions: D:A.265

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

FES.7: 11 residues within 4Å: Chain C: C.129, H.131, L.132, G.133, C.134, C.149, C.151, H.152, G.153, S.154 Chain D: V.161 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.129, C:H.131, C:C.149, C:H.152 FES.15: 10 residues within 4Å: Chain F: C.129, H.131, L.132, G.133, C.134, C.149, C.151, H.152, G.153, S.154 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.129, F:H.131, F:C.149, F:H.152

1 x 6PE: 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)

6PE.11: 10 residues within 4Å: Chain D: M.44, L.110, F.113, R.114, Y.117, Y.118, R.358, F.367, W.368, A.371 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.110, D:F.113, D:F.367 Hydrogen bonds: D:Y.117 Salt bridges: D:R.358

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esser, L. et al., Crystal structure of bacterial cytochromebc1in complex with azoxystrobin reveals a conformational switch of the Rieske iron-sulfur protein subunit. J.Biol.Chem. (2019)

Release Date

2019-06-19

Peptides

Cytochrome b: AD
Cytochrome c1: BE
Ubiquinol-cytochrome c reductase iron-sulfur subunit: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

D
W

B
T

E
X

C
U

F
Y

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

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