SMTL ID : 6zft.1

Crystal structure of bovine cytochrome bc1 in complex with quinolone inhibitor CK-2-68

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-mer

Ligands

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 3 residues within 4Å: Chain A: A.261, Y.384, R.386 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.261, A:R.386 PG4.3: 10 residues within 4Å: Chain A: D.330, F.334, Q.337, Q.428, L.429, P.430, D.431, R.434, G.438 Chain G: F.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.334, A:L.429, A:D.431, A:R.434 PG4.9: 4 residues within 4Å: Chain C: L.120, I.145, F.273 Ligands: PG4.10 No protein-ligand interaction detected (PLIP) PG4.10: 4 residues within 4Å: Chain C: F.127, I.145, L.149 Ligands: PG4.9 No protein-ligand interaction detected (PLIP)

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

6PE.2: 9 residues within 4Å: Chain A: S.437, F.440, L.442 Chain C: H.220, I.225 Chain D: M.221, K.225 Ligands: CDL.4, PX4.18 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:S.437, A:F.440 Hydrophobic interactions: C:I.225 Salt bridges: C:H.220, C:H.220

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.4: 8 residues within 4Å: Chain A: F.334, W.441, L.442, R.443 Chain C: R.4, I.18, H.220 Ligands: 6PE.2 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Salt bridges: C:R.4, C:H.220, A:R.443 Hydrogen bonds: A:L.442 CDL.11: 10 residues within 4Å: Chain C: S.27, S.28, W.29, M.95 Chain F: Q.62 Chain G: R.39, T.40, C.43 Ligands: PEE.12, CDL.15 7 PLIP interactions: 2 interactions with chain C, 1 interactions with chain F, 4 interactions with chain G Hydrogen bonds: C:S.28, C:S.28, F:Q.62 Hydrophobic interactions: G:T.40 Salt bridges: G:R.39, G:R.39, G:R.39 CDL.15: 20 residues within 4Å: Chain C: S.28, N.31, L.35, K.226, G.230, L.233, L.234 Chain D: Y.219, K.222, R.223, K.230 Chain F: R.61, Q.62 Chain G: Y.28, F.29, I.33, N.35, V.36, R.39 Ligands: CDL.11 12 PLIP interactions: 6 interactions with chain D, 4 interactions with chain G, 2 interactions with chain C Hydrophobic interactions: D:Y.219, G:I.33, G:V.36, C:L.35, C:L.233 Hydrogen bonds: D:K.230, D:K.230, G:N.35 Salt bridges: D:K.222, D:R.223, D:K.230, G:R.39 CDL.19: 6 residues within 4Å: Chain E: K.52, S.56, V.59, S.60, S.63 Chain J: R.32 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:S.56, E:S.56, E:S.63 Salt bridges: E:K.52, E:K.52, E:K.52

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

HEM.5: 22 residues within 4Å: Chain C: L.40, Q.43, I.44, G.47, L.48, L.50, A.51, R.79, H.82, A.83, A.86, F.89, T.125, A.126, G.129, Y.130, L.132, P.133, H.181, F.182, P.185, Y.272 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:L.40, C:Q.43, C:I.44, C:L.50, C:A.83, C:A.86, C:F.89, C:T.125, C:L.132, C:F.182, C:F.182 Salt bridges: C:R.79, C:R.79 Metal complexes: C:H.82, C:H.181 HEM.6: 18 residues within 4Å: Chain C: W.30, G.33, L.36, H.96, V.97, R.99, S.105, W.112, G.115, V.116, L.118, L.119, H.195, L.196, L.199, S.204, N.205 Ligands: JHB.7 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:L.36, C:L.36, C:V.97, C:W.112, C:W.112, C:W.112, C:L.118, C:L.119, C:L.196, C:L.199 Hydrogen bonds: C:G.33, C:S.105, C:N.205 Water bridges: C:W.30, C:F.32, C:F.32 Salt bridges: C:H.96, C:R.99, C:R.99 pi-Cation interactions: C:R.99 Metal complexes: C:H.96, C:H.195

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

JHB.7: 16 residues within 4Å: Chain C: A.16, F.17, L.20, I.26, S.34, G.37, I.38, I.41, M.189, M.193, L.196, H.200, S.204, F.219, D.227 Ligands: HEM.6 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.17, C:F.17, C:L.20, C:L.20, C:I.41, C:L.196, C:F.219, C:F.219

1 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.8: 5 residues within 4Å: Chain C: H.344, T.348, Q.351 Chain G: W.60, E.64 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain C Hydrophobic interactions: G:W.60 Hydrogen bonds: C:Q.351, C:Q.351 Salt bridges: C:H.344

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

PEE.12: 16 residues within 4Å: Chain C: W.29, Y.94, G.98, L.101, Y.102, Y.103, M.315, Q.321, F.324, W.325, V.328, L.331 Chain F: Q.62 Chain G: C.43, V.47 Ligands: CDL.11 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.29, C:W.29, C:L.101, C:Y.103, C:F.324, C:W.325, C:V.328, C:L.331 Hydrogen bonds: C:Y.102, C:Y.102, C:Q.321, F:Q.62 PEE.16: 16 residues within 4Å: Chain C: I.77, L.232, I.235, M.239 Chain D: H.199, M.203, K.206, M.207, M.210, M.211 Chain E: Y.49, A.50, N.53, V.54, Q.57 Chain J: D.35 9 PLIP interactions: 1 interactions with chain J, 3 interactions with chain D, 2 interactions with chain E, 3 interactions with chain C Hydrogen bonds: J:D.35 Hydrophobic interactions: D:M.210, E:V.54, E:V.54, C:L.232, C:I.235, C:I.235 Salt bridges: D:H.199, D:K.206

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.13: 5 residues within 4Å: Chain C: T.58, W.134, D.170, A.258, P.260 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.134 PO4.20: 1 residues within 4Å: Chain F: Y.83 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.83, F:Y.83 PO4.21: 3 residues within 4Å: Chain G: R.23, A.24, F.25 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:A.24, G:F.25 PO4.22: 4 residues within 4Å: Chain G: H.27, Y.28, F.29, S.30 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:Y.28, G:F.29, G:S.30, G:S.30 PO4.23: 3 residues within 4Å: Chain G: A.42, L.45, R.46 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:A.42 Salt bridges: G:R.46 PO4.24: 4 residues within 4Å: Chain D: E.3, L.4 Chain H: L.47, H.51 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain H Hydrogen bonds: D:E.3, D:E.3 Salt bridges: H:H.51

1 x HEC: HEME C(Non-covalent)

HEC.14: 18 residues within 4Å: Chain D: V.31, V.35, C.36, C.39, H.40, N.104, L.108, P.109, P.110, I.115, R.119, Y.125, L.130, F.152, I.157, G.158, M.159, P.162 15 PLIP interactions: 15 interactions with chain D, Hydrophobic interactions: D:V.31, D:V.35, D:N.104, D:P.109, D:P.110, D:I.115, D:L.130, D:I.157, D:P.162 Hydrogen bonds: D:Y.125, D:Y.125, D:G.158 Salt bridges: D:R.119 pi-Stacking: D:H.40 Metal complexes: D:H.40

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

FES.17: 10 residues within 4Å: Chain E: C.139, H.141, L.142, G.143, C.144, C.158, C.160, H.161, S.163, P.175 2 PLIP interactions: 2 interactions with chain E, Metal complexes: E:H.141, E:C.158

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

PX4.18: 10 residues within 4Å: Chain A: D.415, F.440 Chain E: Y.37, T.40, T.44 Chain J: F.13, R.14, T.16, F.19 Ligands: 6PE.2 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain J, 3 interactions with chain E Salt bridges: A:D.415 pi-Cation interactions: A:F.440, J:F.19, E:Y.37 Hydrophobic interactions: E:T.44 Hydrogen bonds: E:T.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amporndanai, K. et al., Targeting the ubiquinol-reduction (Qi) site of the mitochondrial cytochrome bc1 complex for the development of next generation quinolone antimalarials. To Be Published

Release Date

2021-06-30

Peptides

Cytochrome b-c1 complex subunit 1, mitochondrial: A
Cytochrome b-c1 complex subunit 2, mitochondrial: B
Cytochrome b: C
Cytochrome c1, heme protein, mitochondrial: D
Cytochrome b-c1 complex subunit Rieske, mitochondrial: E
Cytochrome b-c1 complex subunit 7: F
Cytochrome b-c1 complex subunit 8: G
Cytochrome b-c1 complex subunit 6, mitochondrial: H
Cytochrome b-c1 complex subunit Rieske, mitochondrial: I
Cytochrome b-c1 complex subunit 9: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

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

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