SMTL ID : 5nmi.1

Cytochrome bc1 bound to the inhibitor MJM170

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

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

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 23 residues within 4Å: Chain C: L.34, Q.37, I.38, G.41, L.42, L.44, A.45, Y.48, R.73, H.76, A.77, A.80, T.119, A.120, G.123, Y.124, L.126, P.127, F.172, H.175, F.176, P.179, Y.266 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:L.34, C:Q.37, C:I.38, C:L.44, C:Y.48, C:A.77, C:T.119, C:A.120, C:L.126, C:L.126, C:F.172, C:F.176 Salt bridges: C:R.73, C:R.73 pi-Stacking: C:H.76, C:H.76, C:H.175, C:H.175, C:H.175 Metal complexes: C:H.76, C:H.175 HEM.2: 22 residues within 4Å: Chain C: W.24, G.27, S.28, L.30, G.31, F.83, L.87, H.90, V.91, R.93, S.99, W.106, G.109, V.110, L.112, L.113, H.189, L.190, L.193, S.198, N.199 Ligands: MJM.3 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:L.30, C:L.30, C:F.83, C:V.91, C:V.110, C:L.112, C:L.113, C:L.190, C:L.193, C:L.193 Hydrogen bonds: C:W.24, C:G.27, C:S.99, C:S.99, C:N.199, C:N.199 Salt bridges: C:H.90, C:R.93, C:R.93 pi-Cation interactions: C:R.93 Metal complexes: C:H.90, C:H.189 HEM.13: 23 residues within 4Å: Chain N: L.34, Q.37, I.38, G.41, L.42, L.44, A.45, Y.48, R.73, H.76, A.77, A.80, T.119, A.120, G.123, Y.124, L.126, P.127, F.172, H.175, F.176, P.179, Y.266 19 PLIP interactions: 19 interactions with chain N, Hydrophobic interactions: N:L.34, N:Q.37, N:Q.37, N:I.38, N:L.44, N:Y.48, N:A.77, N:T.119, N:L.126, N:L.126, N:F.172, N:F.176, N:F.176 Salt bridges: N:R.73, N:R.73 pi-Stacking: N:H.76, N:H.175, N:H.175 Metal complexes: N:H.76 HEM.14: 21 residues within 4Å: Chain N: W.24, G.27, L.30, G.31, F.83, L.87, H.90, V.91, R.93, S.99, W.106, G.109, V.110, L.112, L.113, H.189, L.190, L.193, S.198, N.199 Ligands: MJM.15 18 PLIP interactions: 18 interactions with chain N, Hydrophobic interactions: N:L.30, N:L.30, N:F.83, N:V.110, N:L.113, N:L.190, N:L.193, N:L.193 Hydrogen bonds: N:G.27, N:S.99, N:S.99, N:N.199, N:N.199 Salt bridges: N:H.90, N:R.93, N:R.93 Metal complexes: N:H.90, N:H.189

2 x MJM: (4aS)-2-methyl-3-(4-phenoxyphenyl)-5,6,7,8-tetrahydroquinolin-4(4aH)-one(Non-covalent)

MJM.3: 15 residues within 4Å: Chain C: A.10, F.11, L.14, I.20, W.24, S.28, G.31, I.32, I.35, L.190, H.194, S.198, F.213, D.221 Ligands: HEM.2 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.11, C:L.14, C:I.20, C:W.24, C:I.32, C:I.35, C:L.190, C:L.190, C:F.213 Hydrogen bonds: C:S.28 pi-Stacking: C:F.213 MJM.15: 13 residues within 4Å: Chain N: F.11, L.14, A.16, I.20, G.31, I.32, I.35, L.190, H.194, S.198, F.213, D.221 Ligands: HEM.14 9 PLIP interactions: 9 interactions with chain N Hydrophobic interactions: N:F.11, N:L.14, N:A.16, N:I.20, N:I.32, N:I.35, N:L.190, N:F.213 pi-Stacking: N:F.213

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

PEE.4: 14 residues within 4Å: Chain C: W.23, Y.88, M.89, Y.96, Y.97, M.309, Q.315, F.318, W.319, V.322 Chain F: Q.73 Chain G: C.45, V.49 Ligands: CDL.6 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:W.23, C:W.23, C:W.23, C:Y.96, C:Y.96, C:F.318, C:W.319, C:V.322 Hydrogen bonds: C:Y.96 PEE.8: 16 residues within 4Å: Chain C: L.36, M.75, I.229, M.233 Chain D: H.199, M.203, K.206, M.210, L.214 Chain E: Y.127, A.128, N.131, V.132, V.133, Q.135 Chain J: D.37 10 PLIP interactions: 2 interactions with chain C, 3 interactions with chain E, 4 interactions with chain D, 1 interactions with chain J Hydrophobic interactions: C:L.36, C:I.229, E:V.132, E:V.133, D:M.210, D:L.214 Hydrogen bonds: E:Q.135, J:D.37 Salt bridges: D:H.199, D:K.206 PEE.11: 12 residues within 4Å: Chain A: D.416, F.441 Chain D: M.221 Chain E: Y.115, T.118, T.122 Chain J: R.16, T.18, F.21, I.25, V.26 Ligands: CDL.5 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain E Hydrophobic interactions: J:I.25, J:V.26, E:T.118 Hydrogen bonds: J:R.16, E:T.122 PEE.16: 17 residues within 4Å: Chain N: W.23, Y.88, M.89, G.92, Y.96, Y.97, M.309, Q.315, F.318, W.319, V.322, L.325 Chain Q: Q.73 Chain R: C.45, V.49, F.53 Ligands: CDL.18 15 PLIP interactions: 2 interactions with chain R, 12 interactions with chain N, 1 interactions with chain Q Hydrophobic interactions: R:V.49, R:F.53, N:W.23, N:W.23, N:Y.96, N:Y.96, N:F.318, N:W.319, N:W.319, N:V.322, N:V.322, N:L.325 Hydrogen bonds: N:Y.96, N:Y.97, Q:Q.73 PEE.20: 15 residues within 4Å: Chain N: L.36, M.75, I.229, M.233 Chain O: H.199, M.203, K.206, M.207, M.211, L.214 Chain P: Y.127, A.128, N.131, V.132, Q.135 9 PLIP interactions: 3 interactions with chain N, 3 interactions with chain O, 3 interactions with chain P Hydrophobic interactions: N:L.36, N:I.229, N:I.229, O:L.214, P:V.132 Salt bridges: O:H.199, O:K.206 Hydrogen bonds: P:N.131, P:N.131 PEE.21: 9 residues within 4Å: Chain L: F.441 Chain O: M.221 Chain P: Y.115, T.118 Chain U: R.16, T.18, F.21, A.22 Ligands: CDL.17 3 PLIP interactions: 2 interactions with chain U, 1 interactions with chain P Hydrophobic interactions: U:A.22 Hydrogen bonds: U:R.16, P:T.118

6 x CDL: CARDIOLIPIN(Non-covalent)

CDL.5: 12 residues within 4Å: Chain A: D.331, F.335, R.435, S.438, F.441 Chain C: M.4, K.5, N.8, D.13, H.214, I.222 Ligands: PEE.11 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:F.335, C:I.222 Hydrogen bonds: A:S.438, C:N.8 Salt bridges: C:K.5, C:K.5, C:H.214, C:H.214 CDL.6: 10 residues within 4Å: Chain C: S.21, S.22, W.23 Chain F: Q.73 Chain G: V.38, R.41, T.42, C.45 Ligands: PEE.4, CDL.9 9 PLIP interactions: 2 interactions with chain F, 4 interactions with chain G, 3 interactions with chain C Hydrogen bonds: F:Q.73, F:Q.73, G:R.41, C:S.22, C:S.22, C:W.23 Hydrophobic interactions: G:V.38 Salt bridges: G:R.41, G:R.41 CDL.9: 22 residues within 4Å: Chain C: S.22, N.25, L.29, M.82, K.220, L.223, G.224, L.227 Chain D: Y.219, K.222, R.223, K.230 Chain F: M.71, R.72, Q.73 Chain G: P.28, H.29, G.34, N.37, V.38, R.41 Ligands: CDL.6 13 PLIP interactions: 3 interactions with chain G, 6 interactions with chain D, 1 interactions with chain F, 3 interactions with chain C Hydrogen bonds: G:P.28, G:N.37, D:Y.219, D:Y.219, D:K.230, F:R.72, C:S.22 Salt bridges: G:R.41, D:K.222, D:R.223, D:K.230 Hydrophobic interactions: C:L.227, C:L.227 CDL.12: 12 residues within 4Å: Chain N: S.22, N.25, L.29, G.224, L.227 Chain O: Y.219, K.222, R.223 Chain R: G.34, N.37, R.41 Ligands: CDL.18 8 PLIP interactions: 3 interactions with chain O, 3 interactions with chain N, 2 interactions with chain R Hydrogen bonds: O:R.223, R:N.37, R:R.41 Salt bridges: O:K.222, O:K.230 Hydrophobic interactions: N:L.29, N:L.227, N:L.227 CDL.17: 10 residues within 4Å: Chain L: D.332, F.335, R.435, S.438 Chain N: N.8, I.12, D.13, H.214, I.222 Ligands: PEE.21 6 PLIP interactions: 4 interactions with chain N, 2 interactions with chain L Hydrophobic interactions: N:I.12, N:I.222 Salt bridges: N:K.5, N:H.214 Hydrogen bonds: L:S.438, L:S.438 CDL.18: 11 residues within 4Å: Chain N: S.21, S.22, W.23, F.26 Chain Q: Q.73 Chain R: V.38, R.41, T.42, C.45 Ligands: CDL.12, PEE.16 8 PLIP interactions: 3 interactions with chain N, 4 interactions with chain R, 1 interactions with chain Q Hydrophobic interactions: N:F.26, R:T.42 Hydrogen bonds: N:S.22, N:W.23, R:R.41, Q:Q.73 Salt bridges: R:R.41, R:R.41

2 x HEC: HEME C(Covalent)

HEC.7: 19 residues within 4Å: Chain D: V.31, V.35, C.36, C.39, H.40, L.108, P.109, P.110, I.115, R.119, Y.125, L.129, L.130, F.152, I.157, G.158, M.159, P.162, L.189 15 PLIP interactions: 15 interactions with chain D, Hydrophobic interactions: D:V.31, D:P.109, D:P.110, D:I.115, D:L.129, D:L.130, D:I.157, D:M.159, D:P.162, D:L.189 Hydrogen bonds: D:Y.125, D:Y.125, D:G.158 Salt bridges: D:R.119 Metal complexes: D:H.40 HEC.19: 19 residues within 4Å: Chain O: V.31, V.35, C.36, C.39, H.40, L.108, P.109, P.110, I.115, R.119, Y.125, L.129, L.130, F.152, I.157, G.158, M.159, P.162, I.163 16 PLIP interactions: 16 interactions with chain O, Hydrophobic interactions: O:V.31, O:P.109, O:P.109, O:P.110, O:I.115, O:L.129, O:L.130, O:I.157, O:M.159, O:I.163 Hydrogen bonds: O:Y.125, O:G.158 Salt bridges: O:R.119 pi-Stacking: O:H.40 pi-Cation interactions: O:H.40 Metal complexes: O:H.40

1 x FES: FE2/S2 (INORGANIC) CLUSTER(Covalent)

FES.10: 8 residues within 4Å: Chain E: C.217, H.219, L.220, C.222, C.236, C.238, H.239, S.241 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.217, E:H.219, E:C.236, E:H.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McPhillie, M. et al., New paradigms for understanding and step changes in treating active and chronic, persistent apicomplexan infections. Sci Rep (2016)

Release Date

2017-06-14

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
ARG-ASN-TRP-VAL-PRO-THR-ALA-GLN-LEU-TRP-GLY-ALA-VAL-GLY-ALA-VAL-GLY-LEU-VAL-SER-ALA-THR: KV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L
N

B
B

M
O

C
C

N
P

D
D

O
Q

E
E

I
I

P
R

T
V

F
F

Q
S

G
G

R
T

H
H

S
U

J
J

U
W

K
K

V
X

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

ARG-ASN-TRP-VAL-PRO-THR-ALA-GLN-LEU-TRP-GLY-ALA-VAL-GLY-ALA-VAL-GLY-LEU-VAL-SER-ALA-THR

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