SMTL ID : 3l71.1

Cytochrome BC1 complex from chicken with azoxystrobin bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

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

Ligands

6 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.1: 18 residues within 4Å: Chain A: Y.442 Chain C: F.227, I.230 Chain D: M.222, K.226 Chain E: Y.37, T.40, C.44, T.47, A.48, K.52 Chain J: F.11, A.18, V.21, V.22, A.25, E.29 Ligands: PEE.2 9 PLIP interactions: 4 interactions with chain J, 1 interactions with chain D, 3 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: J:A.18, J:V.21, J:V.22, J:A.25, E:T.47, E:A.48 Salt bridges: D:K.226 Hydrogen bonds: E:Y.37, A:Y.442 PEE.2: 4 residues within 4Å: Chain A: Y.442 Chain C: H.222, I.230 Ligands: PEE.1 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.230 Salt bridges: C:H.222, C:H.222 PEE.7: 18 residues within 4Å: Chain C: W.31, F.96, L.97, I.99, Y.104, Y.105, T.317, F.326, W.327, V.330, L.333, L.334, T.337, Y.359 Chain F: Y.29 Chain G: Q.44, V.48 Ligands: CDL.14 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:W.31, C:W.31, C:W.31, C:F.96, C:F.96, C:L.97, C:I.99, C:Y.104, C:Y.104, C:F.326, C:F.326, C:W.327, C:V.330, C:L.333 Hydrogen bonds: C:Y.104, C:Y.104, C:Y.105 PEE.15: 3 residues within 4Å: Chain K: Y.442 Chain M: H.222 Ligands: PEE.21 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain M Hydrogen bonds: K:Y.442 Salt bridges: M:H.222 PEE.21: 19 residues within 4Å: Chain K: Y.442 Chain M: F.227, I.230, L.237 Chain N: M.222, K.226 Chain O: Y.37, T.40, C.44, T.47, A.48, K.52 Chain T: F.11, A.18, V.21, V.22, A.25, E.29 Ligands: PEE.15 9 PLIP interactions: 3 interactions with chain O, 4 interactions with chain T, 1 interactions with chain M, 1 interactions with chain N Hydrophobic interactions: O:T.47, T:A.18, T:V.21, T:V.22, T:A.25, M:L.237 Hydrogen bonds: O:Y.37, O:T.40 Salt bridges: N:K.226 PEE.22: 18 residues within 4Å: Chain M: W.31, F.96, L.97, I.99, Y.104, Y.105, T.317, F.326, W.327, V.330, L.333, L.334, T.337, Y.359 Chain P: Y.29 Chain Q: Q.44, V.48 Ligands: CDL.29 16 PLIP interactions: 15 interactions with chain M, 1 interactions with chain P Hydrophobic interactions: M:W.31, M:W.31, M:F.96, M:F.96, M:L.97, M:I.99, M:Y.104, M:Y.104, M:Y.105, M:F.326, M:F.326, M:W.327, M:V.330, M:L.333 Hydrogen bonds: M:Y.104, P:Y.29

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

HEM.3: 24 residues within 4Å: Chain C: L.42, Q.45, I.46, G.49, L.50, L.52, A.53, Y.56, R.81, H.84, A.85, A.88, L.124, T.127, A.128, G.131, Y.132, L.134, P.135, H.183, F.184, P.187, I.190, Y.274 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:L.42, C:Q.45, C:I.46, C:L.50, C:L.52, C:A.53, C:Y.56, C:A.85, C:A.88, C:L.124, C:T.127, C:L.134, C:L.134, C:F.184, C:I.190 Salt bridges: C:R.81, C:R.81 pi-Stacking: C:H.84, C:H.84, C:H.183 Metal complexes: C:H.84, C:H.183 HEM.4: 24 residues within 4Å: Chain C: W.32, G.35, S.36, L.38, A.39, F.91, H.98, I.99, R.101, S.107, T.113, W.114, G.117, V.118, L.120, L.121, I.190, T.194, H.197, L.198, L.201, S.206, N.207 Ligands: UQ.6 24 PLIP interactions: 24 interactions with chain C, Hydrophobic interactions: C:L.38, C:F.91, C:T.113, C:W.114, C:W.114, C:V.118, C:L.120, C:L.121, C:I.190, C:T.194, C:L.198, C:L.201, C:L.201 Hydrogen bonds: C:G.35, C:S.206, C:N.207 Water bridges: C:W.32, C:F.34, C:S.36 Salt bridges: C:H.98, C:R.101, C:R.101 Metal complexes: C:H.98, C:H.197 HEM.16: 24 residues within 4Å: Chain M: L.42, Q.45, I.46, G.49, L.50, L.52, A.53, Y.56, V.67, R.81, H.84, A.85, L.124, T.127, A.128, G.131, Y.132, L.134, P.135, H.183, F.184, P.187, I.190, Y.274 22 PLIP interactions: 22 interactions with chain M, Hydrophobic interactions: M:L.42, M:Q.45, M:I.46, M:L.50, M:L.52, M:Y.56, M:V.67, M:A.85, M:L.124, M:T.127, M:L.134, M:L.134, M:F.184, M:P.187, M:I.190 Salt bridges: M:R.81, M:R.81 pi-Stacking: M:H.84, M:H.183, M:H.183 Metal complexes: M:H.84, M:H.183 HEM.17: 24 residues within 4Å: Chain M: W.32, G.35, S.36, L.38, A.39, F.91, H.98, I.99, R.101, S.107, T.113, W.114, G.117, V.118, L.120, L.121, I.190, T.194, H.197, L.198, L.201, S.206, N.207 Ligands: UQ.20 26 PLIP interactions: 26 interactions with chain M, Hydrophobic interactions: M:L.38, M:L.38, M:F.91, M:I.99, M:T.113, M:W.114, M:W.114, M:W.114, M:V.118, M:L.120, M:L.121, M:I.190, M:T.194, M:L.198, M:L.201, M:L.201 Hydrogen bonds: M:G.35, M:S.206, M:N.207 Water bridges: M:S.36, M:R.101 Salt bridges: M:H.98, M:R.101, M:R.101 Metal complexes: M:H.98, M:H.197

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

AZO.5: 21 residues within 4Å: Chain C: M.125, A.128, F.129, Y.132, V.133, M.139, S.140, G.143, A.144, I.147, F.151, I.269, K.270, P.271, E.272, Y.274, F.275, A.278, L.295, S.298, V.299 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:F.129, C:Y.132, C:Y.132, C:I.147, C:I.147, C:I.269, C:P.271, C:P.271, C:A.278, C:L.295, C:L.295, C:V.299 Hydrogen bonds: C:E.272 pi-Stacking: C:F.275 AZO.19: 21 residues within 4Å: Chain M: M.125, A.128, F.129, Y.132, V.133, M.139, S.140, G.143, A.144, I.147, F.151, I.269, K.270, P.271, E.272, Y.274, F.275, A.278, L.295, S.298, V.299 14 PLIP interactions: 14 interactions with chain M Hydrophobic interactions: M:F.129, M:Y.132, M:Y.132, M:I.147, M:I.147, M:I.269, M:P.271, M:P.271, M:A.278, M:L.295, M:L.295, M:V.299 Hydrogen bonds: M:E.272 pi-Stacking: M:F.275

2 x UQ: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer(Non-covalent)

UQ.6: 11 residues within 4Å: Chain C: S.18, L.22, I.28, S.36, A.39, L.198, H.202, S.206, F.221, D.229 Ligands: HEM.4 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.39, C:L.198, C:F.221, C:F.221 Hydrogen bonds: C:S.206 UQ.20: 15 residues within 4Å: Chain M: S.18, L.19, L.22, A.24, I.28, S.36, A.39, M.43, L.198, L.201, H.202, S.206, F.221, D.229 Ligands: HEM.17 5 PLIP interactions: 5 interactions with chain M Hydrophobic interactions: M:L.19, M:A.39, M:L.198, M:F.221 Hydrogen bonds: M:S.206

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain C: F.64, V.67, R.81, P.135, N.256, F.257 Chain D: Y.115 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Y.115, C:R.81, C:R.81, C:N.256 GOL.23: 7 residues within 4Å: Chain M: F.64, A.68, R.81, P.135, N.256, F.257 Chain N: Y.115 3 PLIP interactions: 1 interactions with chain N, 2 interactions with chain M Hydrogen bonds: N:Y.115, M:R.81, M:R.81

2 x HEC: HEME C(Covalent)

HEC.9: 19 residues within 4Å: Chain D: V.36, C.37, C.40, H.41, N.105, A.108, L.109, P.110, P.111, I.116, R.120, Y.126, L.131, F.153, I.158, G.159, M.160, P.163, I.164 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:V.36, D:N.105, D:A.108, D:P.110, D:I.116, D:L.131, D:I.158, D:M.160, D:P.163, D:I.164 Hydrogen bonds: D:G.159 Salt bridges: D:R.120 pi-Stacking: D:H.41 Metal complexes: D:H.41 HEC.24: 19 residues within 4Å: Chain N: V.36, C.37, C.40, H.41, N.105, A.108, L.109, P.110, P.111, I.116, R.120, Y.126, L.131, F.153, I.158, G.159, M.160, P.163, I.164 16 PLIP interactions: 16 interactions with chain N, Hydrophobic interactions: N:V.36, N:N.105, N:A.108, N:P.110, N:I.116, N:L.131, N:I.158, N:M.160, N:P.163, N:I.164 Hydrogen bonds: N:Y.126, N:G.159 Salt bridges: N:R.120 pi-Stacking: N:H.41, N:H.41 Metal complexes: N:H.41

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.10: 15 residues within 4Å: Chain C: A.30, N.33, L.231, G.232, L.235 Chain D: Y.220, K.223, R.224 Chain F: H.72, R.73 Chain G: I.29, A.33, L.34, R.40 Ligands: CDL.14 11 PLIP interactions: 1 interactions with chain G, 1 interactions with chain F, 6 interactions with chain D, 3 interactions with chain C Hydrogen bonds: G:R.40 Salt bridges: F:R.73, D:K.223, D:R.224, D:R.224, D:K.231, C:K.228, C:K.228 Hydrophobic interactions: D:Y.220, D:Y.220, C:A.30 CDL.14: 11 residues within 4Å: Chain C: S.29, A.30, W.31, Y.105 Chain F: H.72 Chain G: V.37, R.40, F.41, Q.44 Ligands: PEE.7, CDL.10 7 PLIP interactions: 4 interactions with chain G, 1 interactions with chain F, 2 interactions with chain C Hydrophobic interactions: G:F.41, C:W.31 Salt bridges: G:R.40, G:R.40, G:R.40, F:H.72 Hydrogen bonds: C:A.30 CDL.25: 14 residues within 4Å: Chain M: A.30, N.33, G.232, L.235 Chain N: Y.220, K.223, R.224 Chain P: H.72, R.73 Chain Q: I.29, A.33, L.34, R.40 Ligands: CDL.29 13 PLIP interactions: 4 interactions with chain M, 1 interactions with chain P, 7 interactions with chain N, 1 interactions with chain Q Hydrophobic interactions: M:A.30, N:Y.220, N:Y.220 Hydrogen bonds: M:N.33, N:Y.220, Q:R.40 Salt bridges: M:K.228, M:K.228, P:R.73, N:K.223, N:R.224, N:R.224, N:K.231 CDL.29: 11 residues within 4Å: Chain M: S.29, A.30, W.31, Y.105 Chain P: H.72 Chain Q: V.37, R.40, F.41, Q.44 Ligands: PEE.22, CDL.25 8 PLIP interactions: 1 interactions with chain P, 4 interactions with chain Q, 3 interactions with chain M Salt bridges: P:H.72, Q:R.40, Q:R.40, Q:R.40 Hydrophobic interactions: Q:Q.44, M:W.31 Hydrogen bonds: M:A.30, M:Y.105

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

BOG.11: 12 residues within 4Å: Chain C: Y.76 Chain D: Q.200, R.203, M.204, K.207, I.211 Chain E: Y.49, A.50, N.53, Q.57 Chain J: D.37 Ligands: BOG.12 9 PLIP interactions: 4 interactions with chain D, 2 interactions with chain E, 2 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: D:K.207, D:I.211, E:Y.49 Hydrogen bonds: D:Q.200, E:N.53, C:Y.76, C:Y.76, J:D.37 Salt bridges: D:K.207 BOG.12: 3 residues within 4Å: Chain D: Q.200, R.203 Ligands: BOG.11 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.200, D:R.203, D:R.203 BOG.18: 5 residues within 4Å: Chain C: M.14 Chain M: M.14, L.198, T.199, H.202 1 PLIP interactions: 1 interactions with chain M Salt bridges: M:H.202 BOG.26: 11 residues within 4Å: Chain M: Y.76, L.241 Chain N: Q.200, R.203, M.204, K.207, M.208 Chain O: A.50, N.53, Q.57 Chain T: D.37 7 PLIP interactions: 3 interactions with chain N, 2 interactions with chain O, 1 interactions with chain M, 1 interactions with chain T Hydrophobic interactions: N:K.207, O:A.50 Hydrogen bonds: N:Q.200, O:N.53, M:Y.76, T:D.37 Salt bridges: N:K.207 BOG.27: 2 residues within 4Å: Chain M: Y.76 Chain N: Q.200 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:Q.200

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

FES.13: 10 residues within 4Å: Chain E: C.139, H.141, L.142, 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.28: 10 residues within 4Å: Chain O: C.139, H.141, L.142, C.144, C.158, C.160, H.161, G.162, S.163, P.175 4 PLIP interactions: 4 interactions with chain O, Metal complexes: O:C.139, O:H.141, O:C.158, O:H.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, L. et al., Famoxadone and related inhibitors bind like methoxy acrylate inhibitors in the Qo site of the BC1 compl and fix the rieske iron-sulfur protein in a positio close to but distinct from that seen with stigmatellin and other "DISTAL" Qo inhibitors. To be Published

Release Date

2010-02-02

Peptides

Mitochondrial ubiquinol-cytochrome-c reductase complex core protein i: AK
Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2: BL
Cytochrome b: CM
Mitochondrial cytochrome c1, heme protein: DN
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EO
Mitochondrial ubiquinol-cytochrome c reductase 14 kda protein: FP
Mitochondrial ubiquinol-cytochrome c reductase ubiquinone-binding protein qp-c: GQ
Mitochondrial ubiquinol-cytochrome c reductase 11 kda protein, complex iii subunit viii: HR
Cytochrome b-c1 complex subunit Rieske, mitochondrial: IS
Mitochondrial ubiquinol-cytochrome c reductase 7.2 kda protein: JT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

K
N

B
B

L
O

C
C

M
P

D
D

N
Q

E
E

O
R

F
F

P
S

G
G

Q
T

H
H

R
U

I
I

S
V

J
J

T
W

Membrane

We predict this structure to be a membrane protein.
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Mitochondrial ubiquinol-cytochrome-c reductase complex core protein i

Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2

Cytochrome b

Mitochondrial cytochrome c1, heme protein

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Mitochondrial ubiquinol-cytochrome c reductase 14 kda protein

Mitochondrial ubiquinol-cytochrome c reductase ubiquinone-binding protein qp-c

Mitochondrial ubiquinol-cytochrome c reductase 11 kda protein, complex iii subunit viii

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Mitochondrial ubiquinol-cytochrome c reductase 7.2 kda protein

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