SMTL ID : 3tgu.1

Cytochrome bc1 complex from chicken with pfvs-designed moa inhibitor bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

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

Ligands

2 x UNL: UNKNOWN LIGAND

UNL.1: 1 residues within 4Å: Chain A: L.432 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.432 UNL.16: 1 residues within 4Å: Chain K: L.432 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:L.432, K:L.432

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

HEM.2: 25 residues within 4Å: Chain C: L.42, Q.45, I.46, G.49, L.50, L.52, A.53, V.67, R.81, H.84, A.85, A.88, F.91, L.124, T.127, A.128, G.131, Y.132, L.134, P.135, H.183, F.184, P.187, I.190, Y.274 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:L.42, C:Q.45, C:I.46, C:L.50, C:L.52, C:V.67, C:A.85, C:F.91, 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.183, C:H.183 Metal complexes: C:H.84, C:H.183 HEM.3: 22 residues within 4Å: Chain C: W.32, G.35, S.36, L.38, A.39, H.98, I.99, R.101, S.107, T.113, W.114, G.117, V.118, L.120, I.190, T.194, H.197, L.198, L.201, S.206, N.207 Ligands: UQ.5 24 PLIP interactions: 24 interactions with chain C, Hydrophobic interactions: C:L.38, C:L.38, C:I.99, C:T.113, C:W.114, C:W.114, C:V.118, C:L.120, C:I.190, C:T.194, C:L.198, C:L.201, C:L.201 Hydrogen bonds: C:W.32, C:G.35, C:S.206, C:N.207 Water bridges: 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.18: 24 residues within 4Å: Chain M: L.42, Q.45, I.46, G.49, L.50, L.52, A.53, V.67, R.81, H.84, A.85, F.91, L.124, T.127, A.128, G.131, Y.132, L.134, P.135, H.183, F.184, P.187, I.190, Y.274 23 PLIP interactions: 23 interactions with chain M, Hydrophobic interactions: M:L.42, M:Q.45, M:I.46, M:L.50, M:L.52, M:V.67, M:A.85, M:F.91, M:L.124, M:T.127, M:L.134, M:L.134, M:F.184, M:I.190 Salt bridges: M:R.81, M:R.81 pi-Stacking: M:H.84, M:H.84, M:H.183, M:H.183, M:H.183 Metal complexes: M:H.84, M:H.183 HEM.19: 22 residues within 4Å: Chain M: W.32, G.35, S.36, L.38, A.39, H.98, I.99, R.101, S.107, T.113, W.114, G.117, V.118, L.120, I.190, T.194, H.197, L.198, L.201, S.206, N.207 Ligands: UQ.22 24 PLIP interactions: 24 interactions with chain M, Hydrophobic interactions: M:L.38, M:L.38, M:I.99, M:T.113, M:W.114, M:W.114, M:V.118, M:L.120, M:I.190, M:T.194, M:L.198, M:L.201, M:L.201 Hydrogen bonds: M:W.32, 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 WF3: methyl (2E)-3-methoxy-2-[2-({[6-methyl-3-(trifluoromethyl)quinoxalin-2-yl]oxy}methyl)phenyl]prop-2-enoate(Non-covalent)

WF3.4: 19 residues within 4Å: Chain C: M.125, A.128, F.129, Y.132, V.133, S.140, G.143, A.144, I.147, I.269, K.270, P.271, E.272, Y.274, F.275, A.278, Y.279, L.282, L.295 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:M.125, C:F.129, C:Y.132, C:I.147, C:I.269, C:P.271, C:F.275 Hydrogen bonds: C:E.272 pi-Stacking: C:F.275 WF3.21: 17 residues within 4Å: Chain M: M.125, A.128, F.129, Y.132, V.133, G.143, A.144, I.147, K.270, P.271, E.272, Y.274, F.275, A.278, Y.279, L.282, L.295 8 PLIP interactions: 8 interactions with chain M Hydrophobic interactions: M:M.125, M:F.129, M:Y.132, M:I.147, M:P.271, M:F.275 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.5: 12 residues within 4Å: Chain C: S.18, L.19, L.22, I.28, A.39, L.198, L.201, H.202, S.206, F.221, D.229 Ligands: HEM.3 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.39, C:L.198, C:F.221 Hydrogen bonds: C:S.206 UQ.22: 13 residues within 4Å: Chain M: S.18, L.19, L.22, I.28, A.39, L.198, L.201, H.202, S.206, F.221, Y.225, D.229 Ligands: HEM.19 3 PLIP interactions: 3 interactions with chain M Hydrophobic interactions: M:A.39, M:L.198, M:F.221

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.6: 13 residues within 4Å: Chain C: A.30, N.33, K.228, G.232, L.235 Chain D: Y.220, K.223, R.224, K.231 Chain F: H.72, R.73 Chain G: R.40 Ligands: CDL.15 9 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C, 1 interactions with chain F, 2 interactions with chain G Hydrophobic interactions: D:Y.220, C:A.30 Salt bridges: D:K.223, D:R.224, D:K.231, C:K.228, F:R.73, G:R.40 Hydrogen bonds: G:R.40 CDL.15: 10 residues within 4Å: Chain C: S.29, A.30, W.31, Y.105 Chain F: H.72 Chain G: R.40, F.41, Q.44 Ligands: CDL.6, PEE.7 9 PLIP interactions: 6 interactions with chain G, 1 interactions with chain F, 2 interactions with chain C Hydrophobic interactions: G:F.41, G:F.41, G:Q.44, C:W.31 Hydrogen bonds: G:R.40, C:A.30 Salt bridges: G:R.40, G:R.40, F:H.72 CDL.23: 10 residues within 4Å: Chain M: S.29, A.30, W.31, Y.105 Chain P: H.72 Chain Q: R.40, F.41, Q.44 Ligands: PEE.24, CDL.27 9 PLIP interactions: 1 interactions with chain P, 3 interactions with chain M, 5 interactions with chain Q Salt bridges: P:H.72, Q:R.40, Q:R.40 Hydrophobic interactions: M:W.31, Q:F.41, Q:Q.44 Hydrogen bonds: M:A.30, M:Y.105, Q:R.40 CDL.27: 13 residues within 4Å: Chain M: A.30, N.33, K.228, G.232, L.235 Chain N: Y.220, K.223, R.224, K.231 Chain P: H.72, R.73 Chain Q: R.40 Ligands: CDL.23 10 PLIP interactions: 5 interactions with chain N, 1 interactions with chain P, 2 interactions with chain M, 2 interactions with chain Q Hydrophobic interactions: N:Y.220, N:Y.220, M:A.30 Salt bridges: N:K.223, N:R.224, N:K.231, P:R.73, M:K.228, Q:R.40 Hydrogen bonds: Q:R.40

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

PEE.7: 16 residues within 4Å: Chain C: W.31, F.96, L.97, Y.104, Y.105, F.277, T.317, F.326, W.327, L.333, L.334 Chain F: Y.29 Chain G: R.40, Q.44, V.48 Ligands: CDL.15 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:W.31, C:W.31, C:F.96, C:F.96, C:L.97, C:Y.104, C:Y.104, C:Y.105, C:F.277, C:F.326, C:W.327 Hydrogen bonds: C:Y.104, C:Y.104, C:Y.105 PEE.8: 6 residues within 4Å: Chain A: S.439, Y.442, W.443 Chain C: H.222, I.230 Ligands: PEE.14 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.230 Salt bridges: C:H.222 PEE.14: 16 residues within 4Å: Chain A: Y.442 Chain C: F.227, I.230 Chain D: M.222 Chain E: Y.37, T.40, T.47, A.48, A.50, A.51, K.52 Chain J: F.11, A.18, V.21, E.29 Ligands: PEE.8 11 PLIP interactions: 5 interactions with chain E, 1 interactions with chain D, 3 interactions with chain J, 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: E:T.47, E:A.48, E:A.50, E:A.51, E:K.52, J:A.18, J:V.21, C:I.230 Salt bridges: D:K.226 Hydrogen bonds: J:F.11, A:Y.442 PEE.17: 4 residues within 4Å: Chain K: S.439, Y.442 Chain M: H.222 Ligands: PEE.31 3 PLIP interactions: 1 interactions with chain M, 2 interactions with chain K Salt bridges: M:H.222 Hydrogen bonds: K:S.439, K:Y.442 PEE.24: 17 residues within 4Å: Chain M: W.31, F.96, L.97, Y.104, Y.105, F.277, T.317, F.326, W.327, L.333, L.334, T.337 Chain P: Y.29 Chain Q: Q.44, V.48, F.52 Ligands: CDL.23 15 PLIP interactions: 14 interactions with chain M, 1 interactions with chain Q Hydrophobic interactions: M:W.31, M:W.31, M:F.96, M:L.97, M:Y.104, M:Y.104, M:Y.105, M:F.277, M:F.277, M:F.326, M:W.327, M:W.327, Q:F.52 Hydrogen bonds: M:Y.104, M:Y.105 PEE.31: 20 residues within 4Å: Chain K: Y.442 Chain M: F.227, I.230, L.241 Chain N: M.204, M.222 Chain O: Y.37, T.40, C.44, T.47, A.48, K.52, V.54, Q.57 Chain T: F.11, R.12, V.21, V.22, E.29 Ligands: PEE.17 10 PLIP interactions: 5 interactions with chain O, 2 interactions with chain T, 2 interactions with chain M, 1 interactions with chain N Hydrophobic interactions: O:T.47, O:A.48, O:V.54, T:V.21, T:V.22, M:L.241, M:L.241 Hydrogen bonds: O:Y.37, O:T.40 Salt bridges: N:K.226

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain C: F.64, 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.25: 8 residues within 4Å: Chain M: F.64, V.67, A.68, R.81, P.135, N.256, F.257 Chain N: Y.115 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain N Hydrogen bonds: M:R.81, M:R.81, M:P.135, N:Y.115

2 x HEC: HEME C(Covalent)

HEC.10: 20 residues within 4Å: Chain D: V.32, 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 15 PLIP interactions: 15 interactions with chain D, Hydrophobic interactions: D:V.32, 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, D:H.41 Metal complexes: D:H.41 HEC.26: 20 residues within 4Å: Chain N: V.32, 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.32, 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

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

BOG.11: 11 residues within 4Å: Chain C: Y.76 Chain D: Q.200, R.203, M.204, K.207 Chain E: Y.49, A.50, N.53, Q.57 Chain J: D.37 Ligands: BOG.12 8 PLIP interactions: 3 interactions with chain E, 2 interactions with chain D, 2 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: E:Y.49, E:A.50 Hydrogen bonds: E:N.53, D:Q.200, 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 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.203 BOG.20: 6 residues within 4Å: Chain M: M.14, S.18, I.195, L.198, T.199, H.202 3 PLIP interactions: 3 interactions with chain M Hydrogen bonds: M:S.18, M:S.18 Salt bridges: M:H.202 BOG.28: 12 residues within 4Å: Chain M: Y.76 Chain N: Q.200, R.203, M.204, K.207, M.208 Chain O: Y.49, A.50, N.53, Q.57 Chain T: D.37 Ligands: BOG.29 7 PLIP interactions: 3 interactions with chain O, 3 interactions with chain N, 1 interactions with chain T Hydrophobic interactions: O:Y.49, O:A.50, N:K.207 Hydrogen bonds: O:N.53, N:Q.200, T:D.37 Salt bridges: N:K.207 BOG.29: 3 residues within 4Å: Chain N: Q.200, R.203 Ligands: BOG.28 No protein-ligand interaction detected (PLIP)

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.30: 8 residues within 4Å: Chain O: C.139, H.141, L.142, C.144, C.158, C.160, H.161, S.163 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

Hao, G.F. et al., Computational discovery of picomolar Q(o) site inhibitors of cytochrome bc1 complex. J.Am.Chem.Soc. (2012)

Release Date

2012-07-04

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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