SMTL ID : 6nhh.1

Rhodobacter sphaeroides bc1 with azoxystrobin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-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, I.205, N.279, Y.297 Ligands: AZO.3 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:L.55, A:Q.58, A:A.66, A:Y.69, A:A.101, A:F.104, A:T.142, A:A.143, A:L.149, A:L.149, A:F.195, A:Y.199, A:Y.199, A:P.202 Salt bridges: A:R.94, A:R.94 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 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:L.51, A:L.51, A:F.104, A:I.112, A:T.128, A:W.129, A:W.129, A:I.135, A:Y.136, A:V.209, A:F.216, A:F.216, A:F.216 Hydrogen bonds: A:G.48, 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.11: 30 residues within 4Å: 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, F.105, M.139, T.142, A.143, G.146, Y.147, L.149, P.150, F.195, H.198, Y.199, P.202, I.205, N.279, Y.297 Ligands: AZO.13 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:Q.58, D:I.63, D:Y.69, D:A.98, D:A.101, D:F.104, D:F.104, D:T.142, D:L.149, D:L.149, D:Y.199, D:Y.199, D:I.205 Salt bridges: D:R.94, D:R.94 Metal complexes: D:H.97, D:H.198 HEM.12: 30 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, G.220, N.221, N.222 21 PLIP interactions: 21 interactions with chain D, Hydrophobic interactions: D:L.51, D:L.51, D:F.104, D:I.112, 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:N.222 Salt bridges: D:H.111, D:R.114, D:R.125 Metal complexes: D:H.111, D:H.212

2 x AZO: METHYL (2Z)-2-(2-{[6-(2-CYANOPHENOXY)PYRIMIDIN-4-YL]OXY}PHENYL)-3-METHOXYACRYLATE(Non-covalent)

AZO.3: 24 residues within 4Å: Chain A: M.140, A.143, F.144, Y.147, V.148, M.154, S.155, G.158, A.159, V.161, I.162, L.165, I.292, V.293, P.294, E.295, Y.297, F.298, F.301, Y.302, M.336, F.337, I.340 Ligands: HEM.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.144, A:Y.147, A:I.162, A:I.162, A:I.292, A:P.294, A:P.294, A:F.301, A:F.301, A:Y.302, A:F.337, A:I.340 Hydrogen bonds: A:E.295 pi-Stacking: A:F.298 AZO.13: 24 residues within 4Å: Chain D: M.140, A.143, F.144, Y.147, V.148, M.154, S.155, G.158, A.159, V.161, I.162, L.165, I.292, V.293, P.294, E.295, Y.297, F.298, F.301, Y.302, M.336, F.337, I.340 Ligands: HEM.11 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.162, D:I.162, D:I.292, D:P.294, D:P.294, D:F.301, D:Y.302, D:F.337, D:I.340 Hydrogen bonds: D:E.295 pi-Stacking: D:F.298

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

6PE.4: 12 residues within 4Å: Chain A: N.42, M.44, L.110, F.113, R.114, Y.117, Y.118, R.358, F.367, W.368, A.371, H.431 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.110, A:F.113, A:F.367 Hydrogen bonds: A:Y.117, A:Y.117, A:R.358 Salt bridges: A:R.358 6PE.14: 11 residues within 4Å: Chain D: N.42, M.44, L.110, F.113, R.114, Y.117, Y.118, R.358, F.367, W.368, A.371 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.110, D:F.113, D:F.367 Hydrogen bonds: D:Y.117, D:Y.117 Salt bridges: D:R.358

2 x 8SP: O-[(R)-{[(2R)-2,3-bis(octanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

8SP.5: 20 residues within 4Å: Chain A: S.102, L.103, I.106, Y.273, L.274, V.293, W.296, L.299, V.375, T.378, W.379, A.382 Chain B: F.110, H.111, G.112, G.115, T.116, G.117, I.118, Q.120 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.112, B:G.112, B:Q.120 Hydrophobic interactions: A:I.106, A:L.274, A:L.274 8SP.17: 20 residues within 4Å: Chain D: S.102, L.103, I.106, Y.273, L.274, V.293, W.296, L.299, V.375, T.378, W.379, A.382 Chain E: F.110, H.111, G.112, G.115, T.116, G.117, I.118, Q.120 11 PLIP interactions: 5 interactions with chain E, 6 interactions with chain D Hydrogen bonds: E:G.112, E:G.112, E:G.117, E:Q.120 Salt bridges: E:H.111 Hydrophobic interactions: D:I.106, D:L.274, D:L.274, D:W.296, D:W.296, D:W.296

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

SR.6: 1 residues within 4Å: Chain A: Q.316 No protein-ligand interaction detected (PLIP) SR.9: 6 residues within 4Å: Chain B: D.8, V.9, P.10, F.11, 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.18: 6 residues within 4Å: Chain E: D.8, V.9, P.10, F.11, E.14, 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.7: 14 residues within 4Å: Chain A: V.262, A.265, I.266, F.269, M.270 Chain B: E.14, G.15, P.16, L.121, F.122, N.123, G.124, R.226, K.227 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.15, B:F.122, B:R.226, B:K.227, A:F.269 Hydrophobic interactions: A:A.265, A:I.266, A:F.269 BOG.15: 13 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, Q.120, L.121, G.124, K.227 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:G.15, E:Q.120, E:G.124, E:K.227, D:F.269 Hydrophobic interactions: D:I.266, D:F.269

2 x HEC: HEME C(Covalent)

HEC.8: 27 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, N.162, I.183, A.184, M.185, P.186, P.188, L.189, V.211, L.215 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:V.35, B:P.98, B:I.131, B:L.135, B:I.183, B:A.184, B:M.185, B:P.188, B:L.215 Hydrogen bonds: B:Y.130, B:Y.130, B:A.184 Salt bridges: B:R.107 Metal complexes: B:H.40 HEC.16: 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 14 PLIP interactions: 14 interactions with chain E, Hydrophobic interactions: E:V.35, E:L.94, E:P.98, E:I.131, E:L.135, E:I.183, E:A.184, E:P.188, E:L.215 Hydrogen bonds: E:Y.130, E:Y.130, E:A.184 Salt bridges: E:R.107 Metal complexes: E:H.40

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

FES.10: 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.19: 10 residues within 4Å: Chain F: 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 F, Metal complexes: F:C.129, F:H.131, F:C.149, F:H.152

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
A

D
E

B
B

E
F

C
C

F
G

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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