SMTL ID : 6zfs.1

Crystal structure of bovine cytochrome bc1 in complex with quinolone inhibitor WDH-1U-4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

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

Ligands

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

6PE.1: 8 residues within 4Å: Chain A: S.438, F.441, L.443 Chain C: H.220 Chain D: M.221, K.225 Ligands: CDL.3, PX4.15 8 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: A:L.443, D:K.225 Hydrogen bonds: A:S.438, A:F.441, C:T.224 Salt bridges: D:K.225, C:H.220, C:H.220

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

PO4.2: 7 residues within 4Å: Chain A: D.331, Q.429, L.430, P.431, D.432 Chain C: P.218 Chain G: F.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.430, A:D.432 PO4.12: 2 residues within 4Å: Chain D: G.121, E.123 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.121 Salt bridges: D:R.190 PO4.16: 5 residues within 4Å: Chain E: R.15, P.16, E.17 Chain G: R.24 Ligands: PO4.21 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.17 PO4.19: 2 residues within 4Å: Chain F: P.41, Y.83 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.83 PO4.21: 4 residues within 4Å: Chain G: R.24, A.25, F.26 Ligands: PO4.16 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:A.25, G:F.26, G:F.26 PO4.22: 5 residues within 4Å: Chain G: F.26, H.28, Y.29, F.30, S.31 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:H.28, G:H.28, G:Y.29, G:F.30, G:S.31, G:S.31 PO4.23: 3 residues within 4Å: Chain G: A.43, L.46, R.47 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:A.43 Salt bridges: G:R.47

5 x CDL: CARDIOLIPIN(Non-covalent)

CDL.3: 10 residues within 4Å: Chain A: F.335, F.441, W.442, L.443, R.444 Chain C: R.4, F.17, I.18, H.220 Ligands: 6PE.1 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Salt bridges: C:R.4, C:H.220, A:R.444 Hydrogen bonds: A:L.443 CDL.8: 11 residues within 4Å: Chain C: S.27, S.28, W.29, M.95 Chain F: Q.62 Chain G: V.37, R.40, T.41, C.44 Ligands: PEE.9, CDL.13 7 PLIP interactions: 2 interactions with chain C, 2 interactions with chain F, 3 interactions with chain G Hydrogen bonds: C:S.28, C:S.28, F:Q.62, F:Q.62 Salt bridges: G:R.40, G:R.40, G:R.40 CDL.13: 20 residues within 4Å: Chain C: S.28, L.35, K.226, L.229, G.230, L.233, L.234 Chain D: Y.219, K.222, R.223, K.230 Chain F: R.61 Chain G: Y.29, F.30, G.33, I.34, N.36, V.37, R.40 Ligands: CDL.8 12 PLIP interactions: 3 interactions with chain C, 6 interactions with chain D, 3 interactions with chain G Hydrophobic interactions: C:L.233, D:Y.219, G:I.34 Hydrogen bonds: C:N.31, D:K.230, D:K.230, G:N.36 Salt bridges: C:K.226, D:K.222, D:R.223, D:K.230, G:R.40 CDL.18: 5 residues within 4Å: Chain E: K.52, S.56, V.59, S.60, S.63 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.56, E:S.56 Salt bridges: E:K.52, E:K.52 CDL.20: 2 residues within 4Å: Chain D: H.120 Chain G: Y.59 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.120

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

HEM.4: 25 residues within 4Å: Chain C: L.40, Q.43, I.44, G.47, L.48, L.50, A.51, Y.54, R.79, H.82, A.83, A.86, F.89, T.125, A.126, G.129, Y.130, L.132, P.133, F.178, H.181, F.182, P.185, E.270, Y.272 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:L.40, C:Q.43, C:I.44, C:L.50, C:Y.54, C:A.83, C:A.86, C:F.89, C:T.125, C:A.126, C:L.132, C:L.132, C:F.178, C:F.182, C:F.182 Salt bridges: C:R.79, C:R.79 pi-Stacking: C:H.181 Metal complexes: C:H.82, C:H.181 HEM.5: 23 residues within 4Å: Chain C: W.30, G.33, S.34, L.36, G.37, L.93, H.96, V.97, R.99, S.105, F.108, T.111, W.112, G.115, V.116, L.118, L.119, H.195, L.196, L.199, S.204, N.205 Ligands: JGW.10 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:L.36, C:L.36, C:V.97, C:T.111, C:W.112, C:W.112, C:L.119, C:L.196, C:L.199, C:L.199 Hydrogen bonds: C:G.33, C:S.105, C:S.204, C:N.205 Water bridges: 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 LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.6: 4 residues within 4Å: Chain C: H.344, I.347, T.348, Q.351 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.351

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

PG4.7: 4 residues within 4Å: Chain C: F.127, M.128, I.145, I.163 No protein-ligand interaction detected (PLIP)

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

PEE.9: 17 residues within 4Å: Chain C: W.29, Y.94, M.95, G.98, R.99, Y.102, Y.103, M.315, Q.321, F.324, W.325, V.328, L.331 Chain F: Q.62 Chain G: C.44, V.48 Ligands: CDL.8 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.29, C:W.29, C:W.29, C:Y.102, C:Y.102, C:Y.103, C:F.324, C:W.325, C:W.325, C:V.328, C:L.331 Hydrogen bonds: C:Y.102, C:Y.102, C:Q.321, F:Q.62 PEE.17: 16 residues within 4Å: Chain C: I.77, I.235, M.239 Chain D: H.199, M.203, K.206, M.207, M.210, M.211 Chain E: Y.49, A.50, A.51, N.53, V.54, Q.57 Chain J: D.35 7 PLIP interactions: 3 interactions with chain D, 3 interactions with chain E, 1 interactions with chain J Hydrophobic interactions: D:M.210, E:Y.49, E:V.54 Salt bridges: D:H.199, D:K.206 Hydrogen bonds: E:Q.57, J:D.35

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

JGW.10: 15 residues within 4Å: Chain C: A.16, F.17, L.20, I.26, S.34, G.37, I.41, M.189, M.193, L.196, H.200, S.204, F.219, D.227 Ligands: HEM.5 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.17, C:L.20, C:I.26, C:I.41, C:L.196, C:F.219, C:F.219 pi-Stacking: C:F.219

1 x HEC: HEME C(Non-covalent)

HEC.11: 21 residues within 4Å: Chain D: V.31, V.35, C.36, C.39, H.40, N.104, A.107, L.108, P.109, P.110, L.112, I.115, R.119, Y.125, L.129, L.130, F.152, I.157, G.158, M.159, P.162 16 PLIP interactions: 16 interactions with chain D, Hydrophobic interactions: D:V.31, D:V.35, D:N.104, D:A.107, D:P.109, D:P.110, D:L.112, D:I.115, D:L.129, D:L.130, D:P.162 Hydrogen bonds: D:Y.125, D:Y.125, D:G.158 Salt bridges: D:R.119 Metal complexes: D:H.40

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

FES.14: 9 residues within 4Å: Chain E: C.139, H.141, L.142, C.144, C.158, C.160, H.161, S.163, P.175 3 PLIP interactions: 3 interactions with chain E, Metal complexes: E:C.139, E:H.141, E:C.158

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

PX4.15: 16 residues within 4Å: Chain A: Y.415, D.416, F.441, L.443 Chain D: M.221 Chain E: Y.37, T.40, T.44, V.47 Chain J: F.13, R.14, T.16, F.19, A.20, I.23 Ligands: 6PE.1 8 PLIP interactions: 2 interactions with chain A, 3 interactions with chain E, 3 interactions with chain J Salt bridges: A:D.416 pi-Cation interactions: A:F.441, E:Y.37, J:F.19 Hydrophobic interactions: E:V.47, J:A.20, J:I.23 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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