SMTL ID : 6fo6.1

CryoEM structure of bovine cytochrome bc1 in complex with the anti-malarial inhibitor SCR0911

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

HEM.1: 21 residues within 4Å: Chain D: L.41, Q.44, I.45, G.48, L.49, V.66, R.80, H.83, A.84, A.87, F.91, T.126, A.127, G.130, L.133, P.134, F.179, H.182, F.183, P.186, Y.273 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:L.41, D:I.45, D:A.84, D:F.91, D:T.126, D:A.127, D:L.133, D:F.179, D:F.183, D:F.183 Salt bridges: D:R.80, D:R.80 pi-Cation interactions: D:H.83 Metal complexes: D:H.83 HEM.2: 22 residues within 4Å: Chain D: W.31, G.34, S.35, L.37, L.94, H.97, V.98, R.100, S.106, T.112, W.113, G.116, L.119, L.120, I.189, A.193, H.196, L.197, L.200, S.205, N.206 Ligands: DY2.3 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:L.37, D:L.94, D:V.98, D:W.113, D:W.113, D:L.119, D:L.120, D:I.189, D:A.193, D:L.197, D:L.200 Hydrogen bonds: D:G.34, D:S.106, D:N.206 Salt bridges: D:H.97, D:R.100, D:R.100 pi-Stacking: D:H.196 Metal complexes: D:H.97, D:H.196 HEM.5: 20 residues within 4Å: Chain M: L.41, Q.44, I.45, G.48, L.49, V.66, R.80, H.83, A.84, A.87, F.91, T.126, A.127, G.130, L.133, P.134, F.179, H.182, F.183, P.186 15 PLIP interactions: 15 interactions with chain M, Hydrophobic interactions: M:L.41, M:I.45, M:I.45, M:A.84, M:F.91, M:T.126, M:A.127, M:L.133, M:F.179, M:F.183, M:F.183 Salt bridges: M:R.80, M:R.80 pi-Cation interactions: M:H.83 Metal complexes: M:H.83 HEM.6: 22 residues within 4Å: Chain M: W.31, G.34, S.35, L.37, L.94, H.97, V.98, R.100, S.106, T.112, W.113, G.116, L.119, L.120, I.189, A.193, H.196, L.197, L.200, S.205, N.206 Ligands: DY2.7 20 PLIP interactions: 20 interactions with chain M, Hydrophobic interactions: M:L.37, M:L.94, M:V.98, M:W.113, M:W.113, M:L.119, M:L.120, M:I.189, M:A.193, M:L.197, M:L.200 Hydrogen bonds: M:G.34, M:S.106, M:N.206 Salt bridges: M:H.97, M:R.100, M:R.100 pi-Stacking: M:H.196 Metal complexes: M:H.97, M:H.196

2 x DY2: 7-methoxy-3-methyl-2-[5-[4-(trifluoromethyloxy)phenyl]pyridin-3-yl]quinolin-4-ol(Non-covalent)

DY2.3: 10 residues within 4Å: Chain D: F.18, S.35, G.38, I.39, L.197, H.201, F.220, I.229, A.232 Ligands: HEM.2 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.18, D:I.39, D:L.197 Hydrogen bonds: D:H.201 pi-Stacking: D:F.220 DY2.7: 12 residues within 4Å: Chain M: F.18, I.27, S.35, G.38, I.39, L.197, H.201, F.220, D.228, I.229, A.232 Ligands: HEM.6 5 PLIP interactions: 5 interactions with chain M Hydrophobic interactions: M:F.18, M:L.197, M:D.228 Hydrogen bonds: M:H.201 pi-Stacking: M:F.220

2 x HEC: HEME C(Non-covalent)

HEC.4: 19 residues within 4Å: Chain E: V.120, C.121, C.124, H.125, N.189, A.192, L.193, P.194, P.195, L.197, R.204, Y.210, L.214, L.215, F.237, I.242, G.243, M.244, P.247 10 PLIP interactions: 10 interactions with chain E, Hydrophobic interactions: E:N.189, E:A.192, E:P.194, E:L.197, E:L.214, E:L.215, E:P.247, E:P.247 Salt bridges: E:R.204 Metal complexes: E:H.125 HEC.8: 18 residues within 4Å: Chain N: V.120, C.121, C.124, H.125, N.189, A.192, L.193, P.194, P.195, L.197, R.204, Y.210, L.214, L.215, F.237, I.242, M.244, P.247 10 PLIP interactions: 10 interactions with chain N, Hydrophobic interactions: N:N.189, N:A.192, N:P.194, N:L.197, N:L.214, N:L.215, N:P.247, N:P.247 Salt bridges: N:R.204 Metal complexes: N:H.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amporndanai, K. et al., X-ray and cryo-EM structures of inhibitor-bound cytochromebc1complexes for structure-based drug discovery. IUCrJ (2018)

Release Date

2018-02-28

Peptides

Cytochrome b-c1 complex subunit Rieske, mitochondrial: AJ
Cytochrome b-c1 complex subunit 1, mitochondrial: BK
Cytochrome b-c1 complex subunit 2, mitochondrial: CL
Cytochrome b: DM
Cytochrome c1, heme protein, mitochondrial: EN
Cytochrome b-c1 complex subunit 7: FO
Cytochrome b-c1 complex subunit 8: GP
Cytochrome b-c1 complex subunit 6, mitochondrial: HQ
Cytochrome b-c1 complex subunit 9: IR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

J
R

B
A

K
N

C
B

L
O

D
C

M
P

E
D

N
Q

F
F

O
S

G
G

P
T

H
H

Q
U

I
J

R
W

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b-c1 complex subunit Rieske, mitochondrial

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 7

Cytochrome b-c1 complex subunit 8

Cytochrome b-c1 complex subunit 6, mitochondrial

Cytochrome b-c1 complex subunit 9

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