SMTL ID : 7tz6.1

Structure of mitochondrial bc1 in complex with ck-2-68

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

HEM.1: 28 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, 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, Y.273 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:L.41, C:Q.44, C:A.87, C:L.133, C:L.133, C:F.183, C:F.183 Salt bridges: C:R.80, C:R.80 pi-Stacking: C:H.83, C:H.182 Metal complexes: C:H.83, C:H.182 HEM.2: 29 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, 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 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:L.37, C:F.90, C:W.113, C:W.113, C:L.119, C:L.120, C:L.197, C:L.200 Hydrogen bonds: C:W.31, C:G.34, C:N.206, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 pi-Cation interactions: C:R.100 Metal complexes: C:H.97, C:H.196 HEM.6: 29 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, Y.273 15 PLIP interactions: 15 interactions with chain N, Hydrophobic interactions: N:L.41, N:Q.44, N:A.87, N:F.90, N:T.126, N:L.133, N:F.183, N:F.183 Salt bridges: N:R.80, N:R.80 pi-Stacking: N:H.83, N:H.182, N:H.182 Metal complexes: N:H.83, N:H.182 HEM.7: 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 19 PLIP interactions: 19 interactions with chain N, Hydrophobic interactions: N:L.37, N:L.37, N:L.94, N:W.113, N:L.119, N:L.120, N:L.197, 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 pi-Cation interactions: N:R.100 Metal complexes: N:H.97, N:H.196

2 x JHB: 7-chloranyl-3-methyl-2-[4-[[4-(trifluoromethyloxy)phenyl]methyl]phenyl]-1~{H}-quinolin-4-one(Non-covalent)

JHB.3: 19 residues within 4Å: Chain C: L.121, M.124, A.125, F.128, M.138, W.141, G.142, V.145, I.146, I.268, P.270, F.274, A.277, Y.278, L.281, L.294, I.298 Chain E: C.160, H.161 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:V.145, C:I.146, C:I.268, C:P.270, C:F.274, C:F.274, C:F.274, C:A.277, C:Y.278, C:L.281, C:L.294 Halogen bonds: C:L.121 Hydrogen bonds: E:H.161 JHB.8: 20 residues within 4Å: Chain N: L.121, M.124, A.125, F.128, M.138, W.141, G.142, V.145, I.146, L.149, I.268, P.270, F.274, A.277, Y.278, L.281, L.294, I.298 Chain P: C.160, H.161 12 PLIP interactions: 11 interactions with chain N, 1 interactions with chain P Hydrophobic interactions: N:V.145, N:V.145, N:I.146, N:I.268, N:P.270, N:F.274, N:A.277, N:Y.278, N:L.281 Halogen bonds: N:L.121, N:M.138 Hydrogen bonds: P:H.161

2 x HEC: HEME C(Covalent)

HEC.4: 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 15 PLIP interactions: 15 interactions with chain D, Hydrophobic interactions: D:N.105, D:A.108, D:P.110, D:P.111, D:I.116, D:L.130, D:L.131, D:P.163, D:P.163, D:I.164 Hydrogen bonds: D:Y.126, D:Y.126, D:G.159 Salt bridges: D:R.120 Metal complexes: D:H.41 HEC.9: 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 14 PLIP interactions: 14 interactions with chain O, Hydrophobic interactions: O:N.105, O:P.110, O:P.111, O:I.116, O:L.130, O:L.131, O:I.158, O:M.160, O:I.164 Hydrogen bonds: O:Y.126, O:Y.126, O:G.159 Salt bridges: O:R.120 Metal complexes: O:H.41

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

FES.5: 9 residues within 4Å: Chain E: C.139, H.141, L.142, G.143, C.144, C.158, C.160, H.161, S.163 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.139, E:H.141, E:C.158, E:H.161 FES.10: 9 residues within 4Å: Chain P: C.139, H.141, L.142, C.144, C.158, C.160, H.161, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esser, L. et al., Structure of complex III with bound antimalarial agent CK-2-68 provides insights into selective inhibition of Plasmodium cytochrome bc 1 complexes. J.Biol.Chem. (2023)

Release Date

2023-02-22

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
N

B
B

M
O

C
C

N
P

D
D

O
Q

E
E

P
R

F
F

Q
S

G
G

R
T

H
H

S
U

I
I

T
V

J
J

U
W

K
K

V
X

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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