SMTL ID : 6fo0.1

CryoEM structure of bovine cytochrome bc1 in complex with the anti-malarial compound GSK932121

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

HEM.1: 24 residues within 4Å: Chain C: Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, V.66, R.80, H.83, A.84, A.87, V.123, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, E.271 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:I.45, C:L.51, C:Y.55, C:A.84, C:A.87, C:T.126, C:A.127, C:L.133, C:F.179, C:F.183, C:F.183, C:P.186 Salt bridges: C:R.80, C:R.80 pi-Stacking: C:H.83 pi-Cation interactions: C:H.182 Metal complexes: C:H.182 HEM.2: 24 residues within 4Å: Chain C: W.31, G.34, S.35, L.37, L.41, F.90, 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: G8U.3 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:V.98, C:W.113, C:W.113, C:L.119, C:I.189, C:A.193, C:L.197, C:L.200 Hydrogen bonds: C:S.106, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 Metal complexes: C:H.97, C:H.196 HEM.5: 24 residues within 4Å: Chain M: Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, V.66, R.80, H.83, A.84, A.87, V.123, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, E.271 17 PLIP interactions: 17 interactions with chain M, Hydrophobic interactions: M:I.45, M:L.51, M:Y.55, M:A.84, M:A.87, M:T.126, M:A.127, M:L.133, M:F.179, M:F.183, M:F.183, M:P.186 Salt bridges: M:R.80, M:R.80 pi-Stacking: M:H.83 pi-Cation interactions: M:H.182 Metal complexes: M:H.182 HEM.6: 24 residues within 4Å: Chain M: W.31, G.34, S.35, L.37, L.41, F.90, 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: G8U.7 17 PLIP interactions: 17 interactions with chain M, Hydrophobic interactions: M:L.37, M:L.37, M:V.98, M:W.113, M:W.113, M:L.119, M:I.189, M:A.193, M:L.197, M:L.200 Hydrogen bonds: M:S.106, M:N.206 Salt bridges: M:H.97, M:R.100, M:R.100 Metal complexes: M:H.97, M:H.196

2 x G8U: 3-chloro-6-(hydroxymethyl)-2-methyl-5-{4-[3-(trifluoromethoxy)phenoxy]phenyl}pyridin-4-ol(Non-covalent)

G8U.3: 16 residues within 4Å: Chain C: F.18, L.21, W.31, S.35, G.38, L.41, I.42, M.190, A.193, M.194, L.197, L.200, S.205, F.220, D.228 Ligands: HEM.2 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.42, C:L.197, C:F.220 Hydrogen bonds: C:S.35 pi-Stacking: C:F.18, C:F.220 G8U.7: 17 residues within 4Å: Chain M: F.18, L.21, W.31, S.35, G.38, L.41, I.42, M.190, A.193, M.194, L.197, L.200, S.205, F.220, Y.224, D.228 Ligands: HEM.6 7 PLIP interactions: 7 interactions with chain M Hydrophobic interactions: M:I.42, M:L.197, M:F.220 Hydrogen bonds: M:S.35, M:S.35 pi-Stacking: M:F.18, M:F.220

2 x HEC: HEME C(Non-covalent)

HEC.4: 25 residues within 4Å: Chain D: V.120, C.121, S.123, C.124, H.125, N.189, A.192, L.193, P.194, P.195, L.197, I.200, R.204, Y.210, V.211, L.214, L.215, F.237, I.242, G.243, M.244, A.245, P.247, I.248, V.270 9 PLIP interactions: 9 interactions with chain D, Hydrophobic interactions: D:V.120, D:P.194, D:L.197, D:L.214, D:I.242 Hydrogen bonds: D:Y.210, D:Y.210 Salt bridges: D:R.204 Metal complexes: D:H.125 HEC.8: 24 residues within 4Å: Chain N: V.120, C.121, S.123, C.124, H.125, N.189, A.192, P.194, P.195, L.197, I.200, R.204, Y.210, V.211, L.214, L.215, F.237, I.242, G.243, M.244, A.245, P.247, I.248, V.270 13 PLIP interactions: 13 interactions with chain N, Hydrophobic interactions: N:P.194, N:L.197, N:L.214, N:L.215, N:I.242, N:P.247, N:P.247, N:I.248 Hydrogen bonds: N:L.193, N:Y.210, N:Y.210 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 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
Chain I/V: IS
Cytochrome b-c1 complex subunit 9: JT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

K
A

B
O

L
B

C
P

M
C

D
Q

N
D

E
R

O
E

F
S

P
F

G
T

Q
G

H
U

R
H

I
V

S
I

J
W

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

Chain I/V

Cytochrome b-c1 complex subunit 9

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