SMTL ID : 6xvf.1

Crystal structure of bovine cytochrome bc1 in complex with tetrahydro-quinolone inhibitor JAG021

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

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

Ligands

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

PG4.1: 2 residues within 4Å: Chain A: Y.385, R.387 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.262, A:R.387, A:R.387 PG4.9: 5 residues within 4Å: Chain C: L.120, A.124, I.145, F.273 Ligands: PG4.10 No protein-ligand interaction detected (PLIP) PG4.10: 6 residues within 4Å: Chain C: F.127, M.128, I.145, L.149, I.163 Ligands: PG4.9 No protein-ligand interaction detected (PLIP) PG4.27: 2 residues within 4Å: Chain K: Y.385, R.387 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:A.262, K:R.387, K:R.387 PG4.35: 5 residues within 4Å: Chain M: L.120, A.124, I.145, F.273 Ligands: PG4.36 No protein-ligand interaction detected (PLIP) PG4.36: 6 residues within 4Å: Chain M: F.127, M.128, I.145, L.149, I.163 Ligands: PG4.35 No protein-ligand interaction detected (PLIP)

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

6PE.2: 9 residues within 4Å: Chain A: S.438, F.441, L.443 Chain C: H.220, I.225 Chain D: M.221, K.225 Ligands: CDL.4, PX4.19 7 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: D:K.225, A:L.443 Hydrogen bonds: A:S.438, A:F.441, C:T.224 Salt bridges: C:H.220, C:H.220 6PE.28: 9 residues within 4Å: Chain K: S.438, F.441, L.443 Chain M: H.220, I.225 Chain N: M.221, K.225 Ligands: CDL.30, PX4.45 7 PLIP interactions: 3 interactions with chain K, 3 interactions with chain M, 1 interactions with chain N Hydrophobic interactions: K:L.443, N:K.225 Hydrogen bonds: K:S.438, K:F.441, M:T.224 Salt bridges: M:H.220, M:H.220

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

PO4.3: 7 residues within 4Å: Chain A: D.331, Q.429, L.430, P.431, D.432 Chain C: P.218 Chain G: F.3 Ligand excluded by PLIP PO4.5: 3 residues within 4Å: Chain A: S.290 Chain B: R.66 Chain P: A.98 Ligand excluded by PLIP PO4.14: 6 residues within 4Å: Chain C: G.166, F.167, S.168 Chain O: V.68, M.71, R.92 Ligand excluded by PLIP PO4.16: 2 residues within 4Å: Chain D: E.123, R.190 Ligand excluded by PLIP PO4.20: 5 residues within 4Å: Chain E: R.15, P.16, E.17 Chain G: R.23 Ligands: PO4.24 Ligand excluded by PLIP PO4.23: 3 residues within 4Å: Chain F: P.41, Y.83 Chain L: R.113 Ligand excluded by PLIP PO4.24: 4 residues within 4Å: Chain G: R.23, A.24, F.25 Ligands: PO4.20 Ligand excluded by PLIP PO4.25: 5 residues within 4Å: Chain G: F.25, H.27, Y.28, F.29, S.30 Ligand excluded by PLIP PO4.26: 3 residues within 4Å: Chain G: A.42, L.45, R.46 Ligand excluded by PLIP PO4.29: 7 residues within 4Å: Chain K: D.331, Q.429, L.430, P.431, D.432 Chain M: P.218 Chain Q: F.3 Ligand excluded by PLIP PO4.31: 3 residues within 4Å: Chain F: A.98 Chain K: S.290 Chain L: R.66 Ligand excluded by PLIP PO4.40: 6 residues within 4Å: Chain E: V.68, M.71, R.92 Chain M: G.166, F.167, S.168 Ligand excluded by PLIP PO4.42: 2 residues within 4Å: Chain N: E.123, R.190 Ligand excluded by PLIP PO4.46: 5 residues within 4Å: Chain O: R.15, P.16, E.17 Chain Q: R.23 Ligands: PO4.50 Ligand excluded by PLIP PO4.49: 3 residues within 4Å: Chain B: R.113 Chain P: P.41, Y.83 Ligand excluded by PLIP PO4.50: 4 residues within 4Å: Chain Q: R.23, A.24, F.25 Ligands: PO4.46 Ligand excluded by PLIP PO4.51: 5 residues within 4Å: Chain Q: F.25, H.27, Y.28, F.29, S.30 Ligand excluded by PLIP PO4.52: 3 residues within 4Å: Chain Q: A.42, L.45, R.46 Ligand excluded by PLIP

8 x CDL: CARDIOLIPIN(Non-covalent)

CDL.4: 9 residues within 4Å: Chain A: F.335, W.442, L.443, R.444 Chain C: R.4, F.17, I.18, H.220 Ligands: 6PE.2 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.17 Salt bridges: C:R.4, C:H.220, A:R.444 Hydrogen bonds: A:L.443 CDL.11: 11 residues within 4Å: Chain C: S.27, S.28, W.29, M.95 Chain F: Q.62 Chain G: V.36, R.39, T.40, C.43 Ligands: PEE.12, CDL.17 7 PLIP interactions: 4 interactions with chain G, 2 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: G:T.40 Salt bridges: G:R.39, G:R.39, G:R.39 Hydrogen bonds: C:S.28, C:S.28, F:Q.62 CDL.17: 22 residues within 4Å: Chain C: S.28, N.31, 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, Q.62 Chain G: Y.28, F.29, G.32, I.33, N.35, V.36, R.39 Ligands: CDL.11 15 PLIP interactions: 5 interactions with chain C, 3 interactions with chain G, 7 interactions with chain D Hydrophobic interactions: C:L.35, C:L.233, C:L.233, G:I.33, D:Y.219, D:Y.219 Hydrogen bonds: C:N.31, G:N.35, D:K.230, D:K.230 Salt bridges: C:K.226, G:R.39, D:K.222, D:R.223, D:K.230 CDL.22: 8 residues within 4Å: Chain E: K.52, S.56, V.59, S.60, S.63 Chain M: Y.154, N.158, W.162 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain M Hydrogen bonds: E:S.56, E:S.56, E:S.63, M:N.158 Salt bridges: E:K.52, E:K.52, E:K.52 Hydrophobic interactions: M:Y.154 CDL.30: 9 residues within 4Å: Chain K: F.335, W.442, L.443, R.444 Chain M: R.4, F.17, I.18, H.220 Ligands: 6PE.28 5 PLIP interactions: 2 interactions with chain K, 3 interactions with chain M Hydrogen bonds: K:L.443 Salt bridges: K:R.444, M:R.4, M:H.220 Hydrophobic interactions: M:F.17 CDL.37: 11 residues within 4Å: Chain M: S.27, S.28, W.29, M.95 Chain P: Q.62 Chain Q: V.36, R.39, T.40, C.43 Ligands: PEE.38, CDL.43 7 PLIP interactions: 4 interactions with chain Q, 1 interactions with chain P, 2 interactions with chain M Hydrophobic interactions: Q:T.40 Salt bridges: Q:R.39, Q:R.39, Q:R.39 Hydrogen bonds: P:Q.62, M:S.28, M:S.28 CDL.43: 22 residues within 4Å: Chain M: S.28, N.31, L.35, K.226, L.229, G.230, L.233, L.234 Chain N: Y.219, K.222, R.223, K.230 Chain P: R.61, Q.62 Chain Q: Y.28, F.29, G.32, I.33, N.35, V.36, R.39 Ligands: CDL.37 16 PLIP interactions: 8 interactions with chain N, 3 interactions with chain Q, 5 interactions with chain M Hydrophobic interactions: N:Y.219, N:Y.219, Q:I.33, M:L.35, M:L.233, M:L.233 Hydrogen bonds: N:Y.219, N:K.230, N:K.230, Q:N.35, M:N.31 Salt bridges: N:K.222, N:R.223, N:K.230, Q:R.39, M:K.226 CDL.48: 8 residues within 4Å: Chain C: Y.154, N.158, W.162 Chain O: K.52, S.56, V.59, S.60, S.63 8 PLIP interactions: 6 interactions with chain O, 2 interactions with chain C Hydrogen bonds: O:S.56, O:S.56, O:S.63, C:N.158 Salt bridges: O:K.52, O:K.52, O:K.52 Hydrophobic interactions: C:Y.154

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

HEM.6: 25 residues within 4Å: Chain C: L.40, Q.43, I.44, G.47, L.48, L.50, A.51, Y.54, V.65, 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, Y.272 21 PLIP interactions: 21 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: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.82, C:H.181 pi-Cation interactions: C:H.82 Metal complexes: C:H.82, C:H.181 HEM.7: 24 residues within 4Å: Chain C: W.30, G.33, S.34, L.36, G.37, F.89, 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: JAG.13 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:L.36, C:F.89, 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:N.205 Water bridges: C:W.30, 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 HEM.32: 25 residues within 4Å: Chain M: L.40, Q.43, I.44, G.47, L.48, L.50, A.51, Y.54, V.65, 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, Y.272 21 PLIP interactions: 21 interactions with chain M, Hydrophobic interactions: M:L.40, M:Q.43, M:I.44, M:L.50, M:Y.54, M:A.83, M:F.89, M:T.125, M:A.126, M:L.132, M:L.132, M:F.178, M:F.182, M:F.182 Salt bridges: M:R.79, M:R.79 pi-Stacking: M:H.82, M:H.181 pi-Cation interactions: M:H.82 Metal complexes: M:H.82, M:H.181 HEM.33: 24 residues within 4Å: Chain M: W.30, G.33, S.34, L.36, G.37, F.89, 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: JAG.39 21 PLIP interactions: 21 interactions with chain M, Hydrophobic interactions: M:L.36, M:F.89, M:V.97, M:T.111, M:W.112, M:W.112, M:L.119, M:L.196, M:L.199, M:L.199 Hydrogen bonds: M:G.33, M:S.105, M:N.205 Water bridges: M:W.30, M:F.32 Salt bridges: M:H.96, M:R.99, M:R.99 pi-Cation interactions: M:R.99 Metal complexes: M:H.96, M:H.195

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

LMT.8: 5 residues within 4Å: Chain C: H.344, I.347, T.348, Q.351 Chain G: E.64 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.351, C:Q.351 Salt bridges: C:H.344 LMT.34: 5 residues within 4Å: Chain M: H.344, I.347, T.348, Q.351 Chain Q: E.64 4 PLIP interactions: 4 interactions with chain M Hydrogen bonds: M:T.348, M:Q.351, M:Q.351 Salt bridges: M:H.344

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

PEE.12: 17 residues within 4Å: Chain C: W.29, Y.94, M.95, 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 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.29, C:W.29, C:W.29, C:L.101, 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.21: 10 residues within 4Å: Chain C: I.77 Chain D: H.199, M.203, K.206, M.207, M.210 Chain E: Y.49, N.53, Q.57 Chain J: D.35 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E, 1 interactions with chain J Hydrophobic interactions: D:M.210 Salt bridges: D:H.199, D:K.206 Hydrogen bonds: E:Q.57, J:D.35 PEE.38: 17 residues within 4Å: Chain M: W.29, Y.94, M.95, G.98, L.101, Y.102, Y.103, M.315, Q.321, F.324, W.325, V.328, L.331 Chain P: Q.62 Chain Q: C.43, V.47 Ligands: CDL.37 16 PLIP interactions: 15 interactions with chain M, 1 interactions with chain P Hydrophobic interactions: M:W.29, M:W.29, M:W.29, M:L.101, M:Y.102, M:Y.102, M:Y.103, M:F.324, M:W.325, M:W.325, M:V.328, M:L.331 Hydrogen bonds: M:Y.102, M:Y.103, M:Q.321, P:Q.62 PEE.47: 10 residues within 4Å: Chain M: I.77 Chain N: H.199, M.203, K.206, M.207, M.210 Chain O: Y.49, N.53, Q.57 Chain T: D.35 5 PLIP interactions: 3 interactions with chain N, 1 interactions with chain T, 1 interactions with chain O Hydrophobic interactions: N:M.210 Salt bridges: N:H.199, N:K.206 Hydrogen bonds: T:D.35, O:Q.57

2 x JAG: 2-methyl-3-[4-[4-(trifluoromethyloxy)phenoxy]phenyl]-5,6,7,8-tetrahydro-3~{H}-quinolin-4-one(Non-covalent)

JAG.13: 14 residues within 4Å: Chain C: A.16, F.17, L.20, I.26, S.34, G.37, M.189, M.193, L.196, H.200, S.204, F.219, D.227 Ligands: HEM.7 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.17, C:F.17, C:L.20, C:I.26, C:L.196, C:F.219, C:F.219 pi-Stacking: C:F.219 JAG.39: 14 residues within 4Å: Chain M: A.16, F.17, L.20, I.26, S.34, G.37, M.189, M.193, L.196, H.200, S.204, F.219, D.227 Ligands: HEM.33 8 PLIP interactions: 8 interactions with chain M Hydrophobic interactions: M:F.17, M:F.17, M:L.20, M:I.26, M:L.196, M:F.219, M:F.219 pi-Stacking: M:F.219

2 x HEC: HEME C(Non-covalent)

HEC.15: 22 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, V.126, L.129, L.130, F.152, I.157, G.158, M.159, P.162 17 PLIP interactions: 17 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:V.126, 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 HEC.41: 22 residues within 4Å: Chain N: 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, V.126, L.129, L.130, F.152, I.157, G.158, M.159, P.162 16 PLIP interactions: 16 interactions with chain N, Hydrophobic interactions: N:V.31, N:V.35, N:N.104, N:A.107, N:P.109, N:P.110, N:L.112, N:I.115, N:V.126, N:L.129, N:L.130, N:P.162 Hydrogen bonds: N:Y.125, N:G.158 Salt bridges: N:R.119 Metal complexes: N:H.40

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

FES.18: 9 residues within 4Å: Chain E: C.139, H.141, L.142, 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 FES.44: 9 residues within 4Å: Chain O: C.139, H.141, L.142, C.144, C.158, C.160, H.161, S.163, P.175 2 PLIP interactions: 2 interactions with chain O, Metal complexes: O:H.141, O:C.158

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

PX4.19: 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.2 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 PX4.45: 16 residues within 4Å: Chain K: Y.415, D.416, F.441, L.443 Chain N: M.221 Chain O: Y.37, T.40, T.44, V.47 Chain T: F.13, R.14, T.16, F.19, A.20, I.23 Ligands: 6PE.28 7 PLIP interactions: 3 interactions with chain T, 2 interactions with chain O, 2 interactions with chain K Hydrophobic interactions: T:A.20, T:I.23, O:V.47 pi-Cation interactions: T:F.19, O:Y.37, K:F.441 Salt bridges: K:D.416

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McPhillie, M.J. et al., Potent Tetrahydroquinolone Eliminates Apicomplexan Parasites. Front Cell Infect Microbiol (2020)

Release Date

2020-07-22

Peptides

Cytochrome b-c1 complex subunit 1, mitochondrial: AK
Cytochrome b-c1 complex subunit 2, mitochondrial: BL
Cytochrome b: CM
Cytochrome c1, heme protein, mitochondrial: DN
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EO
Cytochrome b-c1 complex subunit 7: FP
Cytochrome b-c1 complex subunit 8: GQ
Cytochrome b-c1 complex subunit 6, mitochondrial: HR
Cytochrome b-c1 complex subunit Rieske, mitochondrial: IS
Cytochrome b-c1 complex subunit 9: JT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

K
A

B
B

L
B

C
C

M
C

D
D

N
D

E
E

O
E

F
F

P
F

G
G

Q
G

H
H

R
H

I
I

S
I

J
J

T
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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