SMTL ID : 7r3v.1

Crystal structure of bovine Cytochrome bc1 in complex with inhibitor CK-2-67.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

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

Ligands

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

PG4.1: 1 residues within 4Å: Chain A: Y.385 No protein-ligand interaction detected (PLIP) PG4.7: 6 residues within 4Å: Chain C: L.121, A.125, I.146, F.274, L.294 Ligands: PG4.8 No protein-ligand interaction detected (PLIP) PG4.8: 6 residues within 4Å: Chain C: F.128, M.129, I.146, L.150, I.164 Ligands: PG4.7 No protein-ligand interaction detected (PLIP)

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

6PE.2: 8 residues within 4Å: Chain A: S.438, F.441, L.443 Chain C: H.221 Chain D: M.221, K.225 Ligands: CDL.3, PX4.18 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Salt bridges: C:H.221, C:H.221 Hydrogen bonds: A:S.438, A:F.441

3 x CDL: CARDIOLIPIN(Non-covalent)

CDL.3: 11 residues within 4Å: Chain A: F.335, F.441, W.442, L.443, R.444 Chain C: N.3, R.5, I.19, H.221 Ligands: 6PE.2, PO4.13 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Salt bridges: C:R.5, C:H.221, A:R.444 Hydrogen bonds: A:L.443 CDL.16: 18 residues within 4Å: Chain C: S.29, N.32, L.36, K.227, L.230, G.231 Chain D: Y.219, K.222, R.223, K.230 Chain F: R.61, Q.62 Chain G: Y.28, I.33, N.35, V.36, R.39 Ligands: CDL.23 11 PLIP interactions: 4 interactions with chain G, 6 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: G:Y.28, G:I.33, D:Y.219, D:Y.219 Hydrogen bonds: G:N.35, D:K.230 Salt bridges: G:R.39, D:K.222, D:R.223, D:K.230, C:K.227 CDL.23: 10 residues within 4Å: Chain C: S.28, S.29, W.30, M.96 Chain F: Q.62 Chain G: V.36, R.39, T.40 Ligands: PEE.9, CDL.16 8 PLIP interactions: 5 interactions with chain G, 1 interactions with chain F, 2 interactions with chain C Hydrophobic interactions: G:V.36, G:T.40 Hydrogen bonds: G:R.39, F:Q.62, C:S.29, C:S.29 Salt bridges: G:R.39, G:R.39

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

HEM.4: 21 residues within 4Å: Chain C: Q.44, I.45, G.48, L.49, L.51, A.52, 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 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:Q.44, C:L.51, C:A.84, C:F.90, C:T.126, C:A.127, 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.5: 24 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, F.109, T.112, W.113, G.116, V.117, L.119, L.120, H.196, L.197, L.200, S.205, N.206 Ligands: I2Q.10 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:F.90, C:V.98, C:T.112, C:W.113, C:W.113, C:L.119, C:L.120, C:L.197, C:L.200, C:L.200 Hydrogen bonds: C:G.34, C:S.106, C:N.206 Water bridges: C:W.31, C:F.33 Salt bridges: C:H.97, C:R.100, C:R.100 Metal complexes: C:H.97, C:H.196

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

LMT.6: 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:Q.352, C:Q.352 Salt bridges: C:H.345

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

PEE.9: 16 residues within 4Å: Chain C: W.30, Y.95, M.96, G.99, L.102, Y.103, Y.104, M.316, F.325, W.326, V.329, L.332 Chain F: Q.62 Chain G: C.43, V.47 Ligands: CDL.23 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.30, C:W.30, C:L.102, C:Y.104, C:F.325, C:F.325, C:W.326, C:W.326, C:V.329, C:L.332 Hydrogen bonds: C:Y.103, C:Y.103, C:Q.322, F:Q.62 PEE.20: 17 residues within 4Å: Chain C: I.78, I.236, M.240 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: E.31, D.35 9 PLIP interactions: 2 interactions with chain D, 4 interactions with chain E, 2 interactions with chain J, 1 interactions with chain C Hydrophobic interactions: D:M.210, E:V.54, C:I.236 Salt bridges: D:K.206 Hydrogen bonds: E:Y.49, E:N.53, E:Q.57, J:E.31, J:D.35

1 x I2Q: 3-methyl-2-[4-[[4-(trifluoromethoxy)phenyl]methyl]phenyl]-1H-quinolin-4-one(Non-covalent)

I2Q.10: 16 residues within 4Å: Chain C: A.17, F.18, L.21, I.27, S.35, G.38, I.42, M.190, M.194, L.197, H.201, S.205, F.220, D.228 Ligands: HEM.5, DMS.11 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.18, C:I.27, C:I.42, C:L.197 Hydrogen bonds: C:S.35 pi-Stacking: C:F.18, C:F.220, C:F.220

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.11: 5 residues within 4Å: Chain C: M.190, A.193, M.194, L.197 Ligands: I2Q.10 No protein-ligand interaction detected (PLIP)

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

PO4.12: 8 residues within 4Å: Chain C: A.327, A.330, D.331, T.334, L.357 Chain G: P.50, A.53, F.54 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:P.50, G:F.54 PO4.13: 4 residues within 4Å: Chain A: F.335, R.444 Chain C: T.2 Ligands: CDL.3 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.2 Salt bridges: A:R.444 PO4.15: 3 residues within 4Å: Chain D: W.11, E.123, R.190 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.123 Salt bridges: D:R.190 PO4.19: 5 residues within 4Å: Chain E: R.15, P.16, E.17 Chain G: R.23 Ligands: PO4.24 2 PLIP interactions: 2 interactions with chain E Water bridges: E:R.15, E:R.15 PO4.21: 2 residues within 4Å: Chain F: P.41, Y.83 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.83 PO4.22: 7 residues within 4Å: Chain C: W.379 Chain F: R.23, D.24, S.78, L.80, E.81, L.84 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:D.24, F:S.78, F:L.80 Salt bridges: F:R.23 PO4.24: 4 residues within 4Å: Chain G: R.23, A.24, F.25 Ligands: PO4.19 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:A.24, G:F.25, G:F.25 PO4.25: 4 residues within 4Å: Chain G: H.27, Y.28, F.29, S.30 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:H.27, G:F.29, G:S.30 PO4.26: 4 residues within 4Å: Chain F: A.13 Chain G: A.42, L.45, R.46 1 PLIP interactions: 1 interactions with chain G Salt bridges: G:R.46

1 x HEC: HEME C(Covalent)

HEC.14: 23 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, V.185 21 PLIP interactions: 21 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:L.130, D:I.157, D:M.159, D:P.162, D:V.185 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.17: 10 residues within 4Å: Chain E: C.139, H.141, L.142, G.143, C.144, C.158, C.160, H.161, G.162, S.163 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.139, E:H.141, E:C.158, E:H.161

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

PX4.18: 17 residues within 4Å: Chain A: D.416, F.441, L.443 Chain D: M.221 Chain E: Y.37, T.40, T.43, T.44, V.47 Chain J: F.13, R.14, T.16, F.19, A.20, I.23, V.24 Ligands: 6PE.2 9 PLIP interactions: 4 interactions with chain E, 2 interactions with chain A, 3 interactions with chain J Hydrophobic interactions: E:T.43, E:V.47, J:A.20, J:I.23 Hydrogen bonds: E:T.40 pi-Cation interactions: E:Y.37, A:F.441, J:F.19 Salt bridges: A:D.416

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amporndanai, K. et al., Targeting the Ubiquinol-Reduction (Q i ) Site of the Mitochondrial Cytochrome bc 1 Complex for the Development of Next Generation Quinolone Antimalarials. Biology (Basel) (2022)

Release Date

2022-08-10

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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