SMTL ID : 5klv.1

Structure of bos taurus cytochrome bc1 with fenamidone inhibited

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

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

Ligands

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

6PE.1: 10 residues within 4Å: Chain A: S.439, G.440, F.442, W.443, L.444 Chain C: H.221, T.225, I.229 Ligands: CDL.2, PX4.16 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:S.439 Salt bridges: C:H.221, C:H.221 6PE.17: 10 residues within 4Å: Chain K: L.31, T.35, D.36, W.37, R.38, L.39 Chain N: Y.155, I.156, N.159, L.160 5 PLIP interactions: 3 interactions with chain K, 2 interactions with chain N Hydrophobic interactions: K:T.35 Hydrogen bonds: K:R.38, K:L.39, N:Y.155, N:N.159 6PE.18: 10 residues within 4Å: Chain L: S.439, G.440, F.442, W.443, L.444 Chain N: H.221, T.225, I.229 Ligands: CDL.19, PX4.33 3 PLIP interactions: 2 interactions with chain N, 1 interactions with chain L Salt bridges: N:H.221, N:H.221 Hydrogen bonds: L:S.439 6PE.34: 10 residues within 4Å: Chain C: Y.155, I.156, N.159, L.160 Chain V: L.31, T.35, D.36, W.37, R.38, L.39 5 PLIP interactions: 3 interactions with chain V, 2 interactions with chain C Hydrophobic interactions: V:T.35 Hydrogen bonds: V:R.38, V:L.39, C:Y.155, C:N.159

6 x CDL: CARDIOLIPIN(Non-covalent)

CDL.2: 17 residues within 4Å: Chain A: F.336, R.436, F.442, W.443, L.444, R.445 Chain C: N.3, R.5, F.18, I.19, F.220, H.221, T.225 Chain K: W.23, V.26 Ligands: 6PE.1, PX4.16 9 PLIP interactions: 2 interactions with chain K, 4 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: K:W.23, K:W.23 Hydrogen bonds: A:L.444, A:R.445, A:R.445, C:N.3 Salt bridges: A:R.445, C:R.5, C:H.221 CDL.13: 28 residues within 4Å: Chain C: S.29, N.32, F.33, L.36, M.89, K.227, L.230, G.231, L.234, L.235, A.238 Chain D: L.216, P.217, Y.220, K.223, R.224, K.231 Chain F: M.70, R.71, Q.72 Chain G: Y.29, F.30, G.33, I.34, N.36, V.37, R.40 Ligands: CDL.15 14 PLIP interactions: 2 interactions with chain G, 8 interactions with chain D, 4 interactions with chain C Hydrogen bonds: G:N.36, D:Y.220, D:K.231 Salt bridges: G:R.40, D:K.223, D:R.224, D:K.231, C:K.227 Hydrophobic interactions: D:P.217, D:Y.220, D:Y.220, C:N.32, C:F.33, C:L.36 CDL.15: 13 residues within 4Å: Chain C: S.28, S.29, W.30, F.33, M.96, Y.104 Chain F: Q.72 Chain G: V.37, R.40, T.41, C.44 Ligands: 8PE.9, CDL.13 10 PLIP interactions: 3 interactions with chain G, 5 interactions with chain C, 2 interactions with chain F Salt bridges: G:R.40, G:R.40, G:R.40 Hydrophobic interactions: C:W.30, C:W.30, C:F.33 Hydrogen bonds: C:S.29, C:S.29, F:Q.72, F:Q.72 CDL.19: 17 residues within 4Å: Chain L: F.336, R.436, F.442, W.443, L.444, R.445 Chain N: N.3, R.5, F.18, I.19, F.220, H.221, T.225 Chain V: W.23, V.26 Ligands: 6PE.18, PX4.33 9 PLIP interactions: 3 interactions with chain N, 4 interactions with chain L, 2 interactions with chain V Hydrogen bonds: N:N.3, L:L.444, L:R.445, L:R.445 Salt bridges: N:R.5, N:H.221, L:R.445 Hydrophobic interactions: V:W.23, V:W.23 CDL.30: 28 residues within 4Å: Chain N: S.29, N.32, F.33, L.36, M.89, K.227, L.230, G.231, L.234, L.235, A.238 Chain O: L.216, P.217, Y.220, K.223, R.224, K.231 Chain Q: M.70, R.71, Q.72 Chain R: Y.29, F.30, G.33, I.34, N.36, V.37, R.40 Ligands: CDL.32 14 PLIP interactions: 8 interactions with chain O, 4 interactions with chain N, 2 interactions with chain R Hydrophobic interactions: O:P.217, O:Y.220, O:Y.220, N:N.32, N:F.33, N:L.36 Hydrogen bonds: O:Y.220, O:K.231, R:N.36 Salt bridges: O:K.223, O:R.224, O:K.231, N:K.227, R:R.40 CDL.32: 13 residues within 4Å: Chain N: S.28, S.29, W.30, F.33, M.96, Y.104 Chain Q: Q.72 Chain R: V.37, R.40, T.41, C.44 Ligands: 8PE.26, CDL.30 10 PLIP interactions: 5 interactions with chain N, 3 interactions with chain R, 2 interactions with chain Q Hydrophobic interactions: N:W.30, N:W.30, N:F.33 Hydrogen bonds: N:S.29, N:S.29, Q:Q.72, Q:Q.72 Salt bridges: R:R.40, R:R.40, R:R.40

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: Y.284, G.285, G.287 Chain B: A.139, L.140, P.142, Q.143 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.285, B:Q.143 GOL.4: 7 residues within 4Å: Chain B: A.165, Y.168, R.169, A.173 Chain M: R.245, L.430, F.435 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain B Hydrogen bonds: M:R.245, M:R.245, M:L.430, B:Y.168 GOL.5: 8 residues within 4Å: Chain B: K.78, T.128, A.129, P.130, F.132, H.192, V.195, Q.196 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.78, B:H.192, B:Q.196 GOL.20: 7 residues within 4Å: Chain L: Y.284, G.285, G.287 Chain M: A.139, L.140, P.142, Q.143 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain L Hydrogen bonds: M:Q.143, L:G.285 GOL.21: 7 residues within 4Å: Chain B: R.245, L.430, F.435 Chain M: A.165, Y.168, R.169, A.173 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain M Hydrogen bonds: B:R.245, B:R.245, B:L.430, M:Y.168 GOL.22: 8 residues within 4Å: Chain M: K.78, T.128, A.129, P.130, F.132, H.192, V.195, Q.196 3 PLIP interactions: 3 interactions with chain M Hydrogen bonds: M:K.78, M:H.192, M:Q.196

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

HEM.6: 31 residues within 4Å: Chain C: L.41, Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, V.66, R.80, H.83, A.84, A.87, F.90, F.91, V.123, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, F.187, I.189, N.255, Y.273 Ligands: FNM.8 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:L.41, C:Q.44, C:I.45, C:Y.55, C:F.90, C:T.126, C:L.133, C:L.133, C:F.183 Salt bridges: C:R.80, C:R.80 pi-Stacking: C:H.83 Metal complexes: C:H.83, C:H.182 HEM.7: 30 residues within 4Å: Chain C: W.31, G.34, S.35, L.37, G.38, L.41, F.90, L.94, H.97, V.98, R.100, G.101, S.106, Y.107, F.109, T.112, W.113, G.116, V.117, L.119, L.120, V.123, I.189, A.193, H.196, L.197, L.200, S.205, N.206, L.301 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:L.94, C:V.98, C:T.112, C:W.113, C:W.113, C:L.119, C:L.119, C:L.120, C:I.189, C:L.200, C:L.200 Hydrogen bonds: C:W.31, C:G.34, C:S.106, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 Metal complexes: C:H.97, C:H.196 HEM.23: 31 residues within 4Å: Chain N: L.41, Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, V.66, R.80, H.83, A.84, A.87, F.90, F.91, V.123, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, F.187, I.189, N.255, Y.273 Ligands: FNM.25 14 PLIP interactions: 14 interactions with chain N, Hydrophobic interactions: N:L.41, N:Q.44, N:I.45, N:Y.55, N:F.90, N:T.126, N:L.133, N:L.133, N:F.183 Salt bridges: N:R.80, N:R.80 pi-Stacking: N:H.83 Metal complexes: N:H.83, N:H.182 HEM.24: 30 residues within 4Å: Chain N: W.31, G.34, S.35, L.37, G.38, L.41, F.90, L.94, H.97, V.98, R.100, G.101, S.106, Y.107, F.109, T.112, W.113, G.116, V.117, L.119, L.120, V.123, I.189, A.193, H.196, L.197, L.200, S.205, N.206, L.301 22 PLIP interactions: 22 interactions with chain N, Hydrophobic interactions: N:L.37, N:L.37, N:L.94, N:V.98, N:T.112, N:W.113, N:W.113, N:L.119, N:L.119, N:L.120, N:I.189, N:L.200, N:L.200 Hydrogen bonds: N:W.31, N:G.34, N:S.106, N:N.206 Salt bridges: N:H.97, N:R.100, N:R.100 Metal complexes: N:H.97, N:H.196

2 x FNM: (5S)-5-methyl-2-(methylsulfanyl)-5-phenyl-3-(phenylamino)-3,5-dihydro-4H-imidazol-4-one(Non-covalent)

FNM.8: 20 residues within 4Å: Chain C: F.91, M.124, A.127, F.128, Y.131, V.132, M.138, S.139, G.142, A.143, V.145, I.146, I.268, K.269, P.270, E.271, Y.273, F.274, Y.278 Ligands: HEM.6 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.128, C:Y.131, C:I.146, C:P.270, C:E.271 Hydrogen bonds: C:E.271 Water bridges: C:K.269 pi-Stacking: C:F.274 FNM.25: 20 residues within 4Å: Chain N: F.91, M.124, A.127, F.128, Y.131, V.132, M.138, S.139, G.142, A.143, V.145, I.146, I.268, K.269, P.270, E.271, Y.273, F.274, Y.278 Ligands: HEM.23 8 PLIP interactions: 8 interactions with chain N Hydrophobic interactions: N:F.128, N:Y.131, N:I.146, N:P.270, N:E.271 Hydrogen bonds: N:E.271 Water bridges: N:K.269 pi-Stacking: N:F.274

2 x 8PE: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate(Non-covalent)

8PE.9: 30 residues within 4Å: Chain C: W.30, Y.95, M.96, V.98, G.99, R.100, L.102, Y.103, Y.104, P.208, W.272, F.276, L.301, M.316, Q.322, F.325, W.326, L.328, V.329, L.332, L.333, T.336, Y.358 Chain F: Q.72 Chain G: R.39, R.40, C.44, V.48, F.52 Ligands: CDL.15 22 PLIP interactions: 21 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.30, C:W.30, C:Y.95, C:Y.95, C:L.102, C:Y.103, C:Y.103, C:Y.104, C:F.276, C:F.276, C:F.276, C:F.325, C:W.326, C:V.329, C:V.329, C:L.332, C:L.332 Hydrogen bonds: C:W.30, C:Y.103, C:Y.103, C:Y.104, F:Q.72 8PE.26: 30 residues within 4Å: Chain N: W.30, Y.95, M.96, V.98, G.99, R.100, L.102, Y.103, Y.104, P.208, W.272, F.276, L.301, M.316, Q.322, F.325, W.326, L.328, V.329, L.332, L.333, T.336, Y.358 Chain Q: Q.72 Chain R: R.39, R.40, C.44, V.48, F.52 Ligands: CDL.32 22 PLIP interactions: 1 interactions with chain Q, 21 interactions with chain N Hydrogen bonds: Q:Q.72, N:W.30, N:Y.103, N:Y.103, N:Y.104 Hydrophobic interactions: N:W.30, N:W.30, N:Y.95, N:Y.95, N:L.102, N:Y.103, N:Y.103, N:Y.104, N:F.276, N:F.276, N:F.276, N:F.325, N:W.326, N:V.329, N:V.329, N:L.332, N:L.332

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 3 residues within 4Å: Chain C: V.66, R.80, Y.256 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain N: V.66, R.80, Y.256 Ligand excluded by PLIP

2 x HEC: HEME C(Covalent)

HEC.11: 26 residues within 4Å: Chain D: V.32, V.36, C.37, S.39, C.40, H.41, N.105, A.108, L.109, P.110, P.111, L.113, I.116, R.120, Y.126, V.127, L.130, L.131, F.153, I.158, G.159, M.160, P.163, I.164, V.186, L.190 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:N.105, D:P.110, D:P.111, D:I.116, D:L.131, D:F.153, D:I.158, D:M.160, D:P.163, D:P.163, D:I.164, D:L.190 Hydrogen bonds: D:Y.126, D:Y.126, D:G.159 Salt bridges: D:R.120 Metal complexes: D:H.41 HEC.28: 26 residues within 4Å: Chain O: V.32, V.36, C.37, S.39, C.40, H.41, N.105, A.108, L.109, P.110, P.111, L.113, I.116, R.120, Y.126, V.127, L.130, L.131, F.153, I.158, G.159, M.160, P.163, I.164, V.186, L.190 17 PLIP interactions: 17 interactions with chain O, Hydrophobic interactions: O:N.105, O:P.110, O:P.111, O:I.116, O:L.131, O:F.153, O:I.158, O:M.160, O:P.163, O:P.163, O:I.164, O:L.190 Hydrogen bonds: O:Y.126, O:Y.126, O:G.159 Salt bridges: O:R.120 Metal complexes: O:H.41

2 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PEF.12: 34 residues within 4Å: Chain C: L.43, L.46, T.47, F.50, Y.75, I.78, M.82, L.233, I.236, L.239, M.240, L.244 Chain D: H.200, R.203, M.204, K.207, M.208, M.211, M.212, L.215 Chain J: E.32, D.36 Chain K: K.50 Chain P: V.47, Y.49, A.50, A.51, N.53, V.54, V.55, Q.57, F.58, V.59 Ligands: PX4.16 12 PLIP interactions: 2 interactions with chain C, 6 interactions with chain P, 3 interactions with chain D, 1 interactions with chain J Hydrophobic interactions: C:L.43, C:L.46, P:Y.49, P:V.54, P:V.54, P:F.58, P:F.58, D:M.211 Hydrogen bonds: P:Q.57, J:D.36 Salt bridges: D:H.200, D:K.207 PEF.29: 34 residues within 4Å: Chain E: V.47, Y.49, A.50, A.51, N.53, V.54, V.55, Q.57, F.58, V.59 Chain N: L.43, L.46, T.47, F.50, Y.75, I.78, M.82, L.233, I.236, L.239, M.240, L.244 Chain O: H.200, R.203, M.204, K.207, M.208, M.211, M.212, L.215 Chain U: E.32, D.36 Chain V: K.50 Ligands: PX4.33 12 PLIP interactions: 2 interactions with chain N, 6 interactions with chain E, 3 interactions with chain O, 1 interactions with chain U Hydrophobic interactions: N:L.43, N:L.46, E:Y.49, E:V.54, E:V.54, E:F.58, E:F.58, O:M.211 Hydrogen bonds: E:Q.57, U:D.36 Salt bridges: O:H.200, O:K.207

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

FES.14: 11 residues within 4Å: Chain E: C.139, H.141, L.142, G.143, C.144, C.158, C.160, H.161, G.162, S.163, P.175 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.139, E:H.141, E:C.158, E:H.161 FES.31: 11 residues within 4Å: Chain P: C.139, H.141, L.142, G.143, C.144, C.158, C.160, H.161, G.162, S.163, P.175 4 PLIP interactions: 4 interactions with chain P, Metal complexes: P:C.139, P:H.141, P:C.158, P:H.161

2 x PX4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PX4.16: 36 residues within 4Å: Chain A: Y.416, D.417, F.442, L.444 Chain C: I.39, I.229, A.232, L.233, I.236 Chain D: M.222, K.226 Chain J: Y.10, F.14, R.15, R.16, T.17, F.20, A.21, I.24, V.25 Chain K: W.23, V.26, G.27, G.30, L.31, W.33, A.34 Chain P: Y.37, T.40, T.43, T.44, V.47, A.48 Ligands: 6PE.1, CDL.2, PEF.12 13 PLIP interactions: 2 interactions with chain A, 3 interactions with chain P, 5 interactions with chain J, 2 interactions with chain K, 1 interactions with chain C Salt bridges: A:D.417 pi-Cation interactions: A:F.442, P:Y.37, J:F.20 Hydrophobic interactions: P:T.44, J:A.21, J:I.24, J:I.24, J:V.25, K:L.31, K:A.34, C:A.232 Hydrogen bonds: P:T.40 PX4.33: 36 residues within 4Å: Chain E: Y.37, T.40, T.43, T.44, V.47, A.48 Chain L: Y.416, D.417, F.442, L.444 Chain N: I.39, I.229, A.232, L.233, I.236 Chain O: M.222, K.226 Chain U: Y.10, F.14, R.15, R.16, T.17, F.20, A.21, I.24, V.25 Chain V: W.23, V.26, G.27, G.30, L.31, W.33, A.34 Ligands: 6PE.18, CDL.19, PEF.29 13 PLIP interactions: 3 interactions with chain E, 5 interactions with chain U, 2 interactions with chain L, 2 interactions with chain V, 1 interactions with chain N Hydrophobic interactions: E:T.44, U:A.21, U:I.24, U:I.24, U:V.25, V:L.31, V:A.34, N:A.232 Hydrogen bonds: E:T.40 pi-Cation interactions: E:Y.37, U:F.20, L:F.442 Salt bridges: L:D.417

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esser, L. et al., Hydrogen Bonding to the Substrate Is Not Required for Rieske Iron-Sulfur Protein Docking to the Quinol Oxidation Site of Complex III. J.Biol.Chem. (2016)

Release Date

2016-10-12

Peptides

Cytochrome b-c1 complex subunit 1, mitochondrial: AL
Cytochrome b-c1 complex subunit 2, mitochondrial: BM
Cytochrome b: CN
Cytochrome c1, heme protein, mitochondrial: DO
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EP
Cytochrome b-c1 complex subunit 7: FQ
Cytochrome b-c1 complex subunit 8: GR
Cytochrome b-c1 complex subunit 6, mitochondrial: HS
Cytochrome b-c1 complex subunit Rieske, mitochondrial: IT
Cytochrome b-c1 complex subunit 9: JU
Cytochrome b-c1 complex subunit 10: KV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L
A

B
B

M
B

C
C

N
C

D
D

O
D

E
E

P
E

F
F

Q
F

G
G

R
G

H
H

S
H

I
I

T
I

J
J

U
J

K
K

V
K

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b-c1 complex subunit 1, mitochondrial

Cytochrome b-c1 complex subunit 2, mitochondrial

Cytochrome b

Cytochrome c1, heme protein, mitochondrial

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 8

Cytochrome b-c1 complex subunit 6, mitochondrial

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 9

Cytochrome b-c1 complex subunit 10

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