SMTL ID : 9gcx.1

Crystal structure of bovine Cytochrome bc1 in complex with inhibitor F8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.52 Å

Oligo State

hetero-2-2-2-2-4-2-2-2-2-2-mer

Ligands

12 x LOP: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE(Non-covalent)

LOP.1: 10 residues within 4Å: Chain A: S.473, F.476, L.478 Chain C: H.221, I.229 Chain D: K.310 Ligands: CDL.2, LOP.14, PSC.15, LOP.28 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.229 Salt bridges: C:H.221, C:H.221 Hydrogen bonds: A:S.473 LOP.5: 16 residues within 4Å: Chain C: W.30, Y.95, M.96, G.99, Y.103, Y.104, M.316, Q.322, F.325, W.326, V.329, L.332, L.333 Chain F: Q.73 Chain G: V.49 Ligands: CDL.6 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.30, C:W.30, C:Y.103, C:Y.103, C:F.325, C:W.326, C:W.326, C:V.329, C:L.332, C:L.333 Hydrogen bonds: C:Y.103, C:Y.104, C:Q.322 LOP.8: 15 residues within 4Å: Chain C: I.118, L.121, T.122, A.125, F.128, I.146, P.270, F.274, Y.278, L.294, F.296, L.299, A.302, L.303 Ligands: LOP.9 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.118, C:L.121, C:L.121, C:F.296, C:F.296, C:L.299, C:A.302, C:L.303 LOP.9: 16 residues within 4Å: Chain C: F.128, M.129, L.150, W.163, F.178, F.181, L.185, I.188 Chain N: L.43, L.46, F.50, M.190 Chain P: V.132 Ligands: LOP.8, LOP.20, LOP.33 9 PLIP interactions: 4 interactions with chain N, 4 interactions with chain C, 1 interactions with chain P Hydrophobic interactions: N:L.43, N:L.46, N:L.46, N:F.50, C:W.163, C:F.181, C:L.185, C:I.188, P:V.132 LOP.14: 26 residues within 4Å: Chain C: L.43, L.46, T.47, I.78, M.82, L.233, I.236, M.240 Chain D: H.284, M.288, K.291, M.292, M.295, M.296, L.299 Chain E: Y.127, A.128, N.131, V.132, V.133, Q.135, F.136 Chain J: E.33, D.37 Ligands: LOP.1, LOP.28 17 PLIP interactions: 5 interactions with chain C, 5 interactions with chain E, 5 interactions with chain D, 2 interactions with chain J Hydrophobic interactions: C:L.43, C:L.46, C:T.47, C:L.233, C:I.236, E:Y.127, E:V.132, E:V.133, E:F.136, D:K.291, D:M.295, D:L.299 Hydrogen bonds: E:Q.135, J:E.33, J:E.33 Salt bridges: D:H.284, D:K.291 LOP.17: 11 residues within 4Å: Chain C: P.319, L.320, C.323, L.324, L.357 Chain F: W.20 Chain G: A.44, L.47, R.48, P.51, P.52 7 PLIP interactions: 4 interactions with chain G, 2 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: G:P.51, G:P.51, G:P.52, C:L.324, C:L.357, F:W.20 Salt bridges: G:R.48 LOP.20: 10 residues within 4Å: Chain L: S.473, F.476, L.478 Chain N: H.221, I.229 Chain O: K.310 Ligands: LOP.9, CDL.21, LOP.33, PSC.34 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain L Hydrophobic interactions: N:I.229 Salt bridges: N:H.221, N:H.221 Hydrogen bonds: L:S.473 LOP.24: 16 residues within 4Å: Chain N: W.30, Y.95, M.96, G.99, Y.103, Y.104, M.316, Q.322, F.325, W.326, V.329, L.332, L.333 Chain Q: Q.73 Chain R: V.49 Ligands: CDL.25 12 PLIP interactions: 12 interactions with chain N Hydrophobic interactions: N:W.30, N:W.30, N:Y.103, N:Y.103, N:F.325, N:W.326, N:W.326, N:V.329, N:L.332, N:L.333 Hydrogen bonds: N:Y.104, N:Q.322 LOP.27: 15 residues within 4Å: Chain N: I.118, L.121, T.122, A.125, F.128, I.146, P.270, F.274, Y.278, L.294, F.296, L.299, A.302, L.303 Ligands: LOP.28 8 PLIP interactions: 8 interactions with chain N Hydrophobic interactions: N:I.118, N:L.121, N:L.121, N:F.296, N:F.296, N:L.299, N:A.302, N:L.303 LOP.28: 16 residues within 4Å: Chain C: L.43, L.46, F.50, M.190 Chain E: V.132 Chain N: F.128, M.129, L.150, W.163, F.178, F.181, L.185, I.188 Ligands: LOP.1, LOP.14, LOP.27 9 PLIP interactions: 4 interactions with chain N, 4 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: N:W.163, N:F.181, N:L.185, N:I.188, C:L.43, C:L.46, C:L.46, C:F.50, E:V.132 LOP.33: 26 residues within 4Å: Chain N: L.43, L.46, T.47, I.78, M.82, L.233, I.236, M.240 Chain O: H.284, M.288, K.291, M.292, M.295, M.296, L.299 Chain P: Y.127, A.128, N.131, V.132, V.133, Q.135, F.136 Chain U: E.33, D.37 Ligands: LOP.9, LOP.20 16 PLIP interactions: 1 interactions with chain U, 5 interactions with chain O, 5 interactions with chain N, 5 interactions with chain P Hydrogen bonds: U:E.33, P:Q.135 Hydrophobic interactions: O:K.291, O:M.295, O:L.299, N:L.43, N:L.46, N:T.47, N:L.233, N:I.236, P:Y.127, P:V.132, P:V.133, P:F.136 Salt bridges: O:H.284, O:K.291 LOP.36: 11 residues within 4Å: Chain N: P.319, L.320, C.323, L.324, L.357 Chain Q: W.20 Chain R: A.44, L.47, R.48, P.51, P.52 7 PLIP interactions: 2 interactions with chain N, 1 interactions with chain Q, 4 interactions with chain R Hydrophobic interactions: N:L.324, N:L.357, Q:W.20, R:P.51, R:P.51, R:P.52 Salt bridges: R:R.48

6 x CDL: CARDIOLIPIN(Non-covalent)

CDL.2: 16 residues within 4Å: Chain A: F.370, W.477, L.478, R.479 Chain C: R.5, M.11, V.14, F.18, I.19, F.220, H.221, T.225, D.228 Ligands: LOP.1, 01.7, PSC.15 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:V.14, C:F.18, C:F.18, C:F.18, C:I.19, C:I.19, C:F.220, C:T.225, C:D.228 Hydrogen bonds: C:N.3, A:L.478, A:R.479, A:R.479 Salt bridges: C:R.5, C:H.221, A:R.479 CDL.6: 19 residues within 4Å: Chain C: S.28, S.29, W.30, Y.104, L.234, L.237, A.238 Chain F: Q.73 Chain G: V.38, R.41, T.42, C.45, I.46, V.49, A.50, F.53, Y.57 Ligands: LOP.5, CDL.12 19 PLIP interactions: 7 interactions with chain C, 2 interactions with chain F, 10 interactions with chain G Hydrophobic interactions: C:W.30, C:L.237, C:A.238, G:V.38, G:I.46, G:V.49, G:A.50, G:F.53, G:Y.57, G:Y.57 Hydrogen bonds: C:S.29, C:S.29, C:Y.104, C:Y.104, F:Q.73, F:Q.73 Salt bridges: G:R.41, G:R.41, G:R.41 CDL.12: 28 residues within 4Å: Chain C: S.29, N.32, L.36, M.89, K.227, L.230, G.231, L.234, L.235 Chain D: L.293, L.294, M.296, G.297, L.300, Y.304, K.307, R.308, K.315 Chain F: R.72, Q.73 Chain G: F.27, Y.30, F.31, G.34, N.37, V.38, R.41 Ligands: CDL.6 21 PLIP interactions: 6 interactions with chain C, 7 interactions with chain G, 7 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: C:N.32, C:L.36, C:L.230, C:L.234, C:L.234, G:F.27, G:F.27, G:Y.30, G:F.31, G:F.31, D:L.294, D:Y.304 Salt bridges: C:K.227, G:R.41, D:K.307, D:K.307, D:R.308, D:K.315 Hydrogen bonds: G:N.37, D:K.315, F:R.72 CDL.21: 16 residues within 4Å: Chain L: F.370, W.477, L.478, R.479 Chain N: R.5, M.11, V.14, F.18, I.19, F.220, H.221, T.225, D.228 Ligands: LOP.20, 01.26, PSC.34 16 PLIP interactions: 12 interactions with chain N, 4 interactions with chain L Hydrophobic interactions: N:V.14, N:F.18, N:F.18, N:F.18, N:I.19, N:I.19, N:F.220, N:T.225, N:D.228 Hydrogen bonds: N:N.3, L:L.478, L:R.479, L:R.479 Salt bridges: N:R.5, N:H.221, L:R.479 CDL.25: 19 residues within 4Å: Chain N: S.28, S.29, W.30, Y.104, L.234, L.237, A.238 Chain Q: Q.73 Chain R: V.38, R.41, T.42, C.45, I.46, V.49, A.50, F.53, Y.57 Ligands: LOP.24, CDL.31 18 PLIP interactions: 6 interactions with chain N, 10 interactions with chain R, 2 interactions with chain Q Hydrophobic interactions: N:W.30, N:L.237, N:A.238, R:V.38, R:I.46, R:V.49, R:A.50, R:F.53, R:Y.57, R:Y.57 Hydrogen bonds: N:S.29, N:S.29, N:Y.104, Q:Q.73, Q:Q.73 Salt bridges: R:R.41, R:R.41, R:R.41 CDL.31: 28 residues within 4Å: Chain N: S.29, N.32, L.36, M.89, K.227, L.230, G.231, L.234, L.235 Chain O: L.293, L.294, M.296, G.297, L.300, Y.304, K.307, R.308, K.315 Chain Q: R.72, Q.73 Chain R: F.27, Y.30, F.31, G.34, N.37, V.38, R.41 Ligands: CDL.25 23 PLIP interactions: 8 interactions with chain R, 8 interactions with chain O, 1 interactions with chain Q, 6 interactions with chain N Hydrophobic interactions: R:F.27, R:F.27, R:Y.30, R:F.31, R:F.31, O:L.294, O:Y.304, N:N.32, N:L.36, N:L.230, N:L.234, N:L.234 Hydrogen bonds: R:Y.30, R:N.37, O:Y.304, O:K.315, Q:R.72 Salt bridges: R:R.41, O:K.307, O:K.307, O:R.308, O:K.315, N:K.227

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

HEM.3: 22 residues within 4Å: Chain C: Q.44, I.45, G.48, L.49, L.51, Y.55, V.66, R.80, H.83, A.84, A.87, F.90, T.126, A.127, G.130, Y.131, L.133, P.134, H.182, F.183, P.186, Y.273 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:Q.44, C:L.51, C:Y.55, C:V.66, C:A.84, C:A.87, C:F.90, C:T.126, C:L.133, C:L.133, C:F.183, C:F.183 Salt bridges: C:R.80, C:R.80 Metal complexes: C:H.83, C:H.182 HEM.4: 23 residues within 4Å: Chain C: W.31, G.34, S.35, L.37, G.38, F.90, L.94, H.97, V.98, R.100, S.106, T.112, W.113, G.116, V.117, L.119, L.120, H.196, L.197, L.200, S.205, N.206 Ligands: 01.7 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:F.90, C:T.112, C:W.113, C:W.113, C:L.119, C:L.120, C:L.197, C:L.200 Hydrogen bonds: C:G.34, C:S.106, C:S.106, C:N.206, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 Metal complexes: C:H.97, C:H.196 HEM.22: 22 residues within 4Å: Chain N: Q.44, I.45, G.48, L.49, L.51, Y.55, V.66, R.80, H.83, A.84, A.87, F.90, T.126, A.127, G.130, Y.131, L.133, P.134, H.182, F.183, P.186, Y.273 16 PLIP interactions: 16 interactions with chain N, Hydrophobic interactions: N:Q.44, N:L.51, N:Y.55, N:V.66, N:A.84, N:A.87, N:F.90, N:T.126, N:L.133, N:L.133, N:F.183, N:F.183 Salt bridges: N:R.80, N:R.80 Metal complexes: N:H.83, N:H.182 HEM.23: 23 residues within 4Å: Chain N: W.31, G.34, S.35, L.37, G.38, F.90, L.94, H.97, V.98, R.100, S.106, T.112, W.113, G.116, V.117, L.119, L.120, H.196, L.197, L.200, S.205, N.206 Ligands: 01.26 20 PLIP interactions: 20 interactions with chain N, Hydrophobic interactions: N:L.37, N:L.37, N:F.90, N:T.112, N:W.113, N:W.113, N:L.119, N:L.120, N:L.197, N:L.200 Hydrogen bonds: N:G.34, N:S.106, N:S.106, N:N.206, N:N.206 Salt bridges: N:H.97, N:R.100, N:R.100 Metal complexes: N:H.97, N:H.196

2 x 01: 2-methyl-3-(4-(4-(trifluoromethoxy)phenoxy)phenyl)-1,5,7,8-tetrahydro-4H-pyrano[4,3-b]pyridin-4-one

01.7: 15 residues within 4Å: Chain C: A.17, F.18, L.21, I.27, W.31, S.35, G.38, I.39, I.42, M.190, S.205, F.220, D.228 Ligands: CDL.2, HEM.4 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.18, C:L.21, C:F.220 Hydrogen bonds: C:S.205 pi-Stacking: C:F.18, C:F.220 01.26: 15 residues within 4Å: Chain N: A.17, F.18, L.21, I.27, W.31, S.35, G.38, I.39, I.42, M.190, S.205, F.220, D.228 Ligands: CDL.21, HEM.23 6 PLIP interactions: 6 interactions with chain N Hydrophobic interactions: N:F.18, N:L.21, N:F.220 Hydrogen bonds: N:S.205 pi-Stacking: N:F.18, N:F.220

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

LMT.10: 4 residues within 4Å: Chain C: H.345, I.348, T.349, Q.352 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.345, C:T.349, C:Q.352 LMT.29: 4 residues within 4Å: Chain N: H.345, I.348, T.349, Q.352 3 PLIP interactions: 3 interactions with chain N Hydrogen bonds: N:H.345, N:T.349, N:Q.352

2 x HEC: HEME C(Covalent)

HEC.11: 23 residues within 4Å: Chain D: V.116, V.120, C.121, S.123, C.124, H.125, N.189, A.192, L.193, P.194, P.195, I.200, R.204, Y.210, V.211, L.214, L.215, F.237, I.242, G.243, M.244, P.247, I.248 23 PLIP interactions: 23 interactions with chain D, Hydrophobic interactions: D:V.116, D:V.120, D:N.189, D:A.192, D:P.194, D:P.194, D:P.195, D:I.200, D:V.211, D:L.214, D:L.215, D:I.242, D:M.244, D:P.247, D:I.248 Hydrogen bonds: D:Y.210, D:Y.210, D:G.243 Salt bridges: D:R.204 pi-Stacking: D:H.125, D:H.125 pi-Cation interactions: D:H.125 Metal complexes: D:H.125 HEC.30: 23 residues within 4Å: Chain O: V.116, V.120, C.121, S.123, C.124, H.125, N.189, A.192, L.193, P.194, P.195, I.200, R.204, Y.210, V.211, L.214, L.215, F.237, I.242, G.243, M.244, P.247, I.248 22 PLIP interactions: 22 interactions with chain O, Hydrophobic interactions: O:V.116, O:V.120, O:N.189, O:A.192, O:P.194, O:P.194, O:P.195, O:I.200, O:V.211, O:L.214, O:L.215, O:I.242, O:M.244, O:P.247, O:I.248 Hydrogen bonds: O:Y.210, O:G.243 Salt bridges: O:R.204 pi-Stacking: O:H.125, O:H.125 pi-Cation interactions: O:H.125 Metal complexes: O:H.125

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

FES.13: 11 residues within 4Å: Chain E: C.217, H.219, L.220, G.221, C.222, C.236, C.238, H.239, G.240, S.241, P.253 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.217, E:H.219, E:C.236, E:H.239 FES.32: 11 residues within 4Å: Chain P: C.217, H.219, L.220, G.221, C.222, C.236, C.238, H.239, G.240, S.241, P.253 4 PLIP interactions: 4 interactions with chain P, Metal complexes: P:C.217, P:H.219, P:C.236, P:H.239

2 x PSC: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE(Non-covalent)

PSC.15: 16 residues within 4Å: Chain A: D.451, F.476, L.478 Chain D: M.306 Chain E: Y.115, T.118, T.122, V.125 Chain J: F.15, R.16, T.18, F.21 Chain K: W.34, A.35 Ligands: LOP.1, CDL.2 8 PLIP interactions: 4 interactions with chain E, 1 interactions with chain K, 2 interactions with chain A, 1 interactions with chain J Hydrophobic interactions: E:T.122, E:V.125, K:A.35 Hydrogen bonds: E:T.118 pi-Cation interactions: E:Y.115, A:F.476, J:F.21 Salt bridges: A:D.451 PSC.34: 16 residues within 4Å: Chain L: D.451, F.476, L.478 Chain O: M.306 Chain P: Y.115, T.118, T.122, V.125 Chain U: F.15, R.16, T.18, F.21 Chain V: W.34, A.35 Ligands: LOP.20, CDL.21 7 PLIP interactions: 2 interactions with chain L, 3 interactions with chain P, 1 interactions with chain V, 1 interactions with chain U Salt bridges: L:D.451 pi-Cation interactions: L:F.476, P:Y.115, U:F.21 Hydrophobic interactions: P:T.122, P:V.125, V:A.35

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.16: 3 residues within 4Å: Chain F: P.52, Y.94 Chain M: R.148 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain M Hydrogen bonds: F:Y.94, F:Y.94 Salt bridges: M:R.148 SO4.18: 4 residues within 4Å: Chain G: H.29, Y.30, F.31, S.32 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:Y.30, G:F.31, G:S.32 SO4.19: 3 residues within 4Å: Chain G: R.25, A.26, F.27 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:A.26, G:F.27 Salt bridges: G:R.25 SO4.35: 3 residues within 4Å: Chain B: R.148 Chain Q: P.52, Y.94 2 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain B Hydrogen bonds: Q:Y.94 Salt bridges: B:R.148 SO4.37: 4 residues within 4Å: Chain R: H.29, Y.30, F.31, S.32 3 PLIP interactions: 3 interactions with chain R Hydrogen bonds: R:Y.30, R:F.31, R:S.32 SO4.38: 3 residues within 4Å: Chain R: R.25, A.26, F.27 3 PLIP interactions: 3 interactions with chain R Hydrogen bonds: R:A.26, R:F.27 Salt bridges: R:R.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ge, S. et al., Novel antimalarial 3-substituted quinolones isosteres with improved pharmacokinetic properties. Eur.J.Med.Chem. (2024)

Release Date

2025-01-22

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: EIPT
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 9: JU
Cytochrome b-c1 complex subunit 10: KV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L
A

B
B

M
B

C
C

N
C

D
D

O
D

E
E

I
I

P
E

T
I

F
F

Q
F

G
G

R
G

H
H

S
H

J
J

U
J

K
K

V
K

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 9

Cytochrome b-c1 complex subunit 10

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