SMTL ID : 4d6u.1 (1 other biounit)

Cytochrome bc1 bound to the 4(1H)-pyridone GSK932121

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.09 Å

Oligo State

hetero-1-1-1-1-2-1-1-1-1-mer

Ligands

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

HEM.1: 22 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, T.126, A.127, G.130, Y.131, L.133, P.134, H.182, F.183, P.186, Y.273 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:Q.44, C:I.45, C:L.51, C:L.51, C:Y.55, C:A.84, C:A.87, C:T.126, C:A.127, C:L.133, C:F.183, C:F.183, C:P.186 Salt bridges: C:R.80, C:R.80 Metal complexes: C:H.83, C:H.182 HEM.2: 21 residues within 4Å: Chain C: W.31, G.34, S.35, L.37, G.38, L.94, H.97, V.98, R.100, S.106, W.113, G.116, V.117, L.119, L.120, H.196, L.197, L.200, S.205, N.206 Ligands: G8U.3 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:L.94, C:V.98, C:V.117, C:L.119, C:L.119, C:L.120, C:L.197, C:L.200 Hydrogen bonds: C:G.34, C:S.106, C:S.205, C:S.205, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 pi-Cation interactions: C:R.100 Metal complexes: C:H.97, C:H.196

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

G8U.3: 13 residues within 4Å: Chain C: F.18, L.21, W.31, S.35, I.42, A.193, M.194, L.197, H.201, S.205, F.220, D.228 Ligands: HEM.2 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.18, C:I.42, C:F.220 Hydrogen bonds: C:S.205

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

PO4.4: 5 residues within 4Å: Chain A: S.473, F.476, R.479 Chain C: H.221 Ligands: PO4.12 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.473 Salt bridges: C:H.221 PO4.7: 2 residues within 4Å: Chain E: S.138 Ligands: PO4.9 No protein-ligand interaction detected (PLIP) PO4.8: 1 residues within 4Å: Chain D: R.99 No protein-ligand interaction detected (PLIP) PO4.9: 4 residues within 4Å: Chain C: Y.75 Chain E: S.134, Q.135 Ligands: PO4.7 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:Y.75, C:Y.75, E:S.134 PO4.12: 4 residues within 4Å: Chain A: F.476 Chain E: Y.115, T.118 Ligands: PO4.4 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.115, E:T.118 PO4.13: 2 residues within 4Å: Chain F: R.50, Y.94 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.94, F:Y.94

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

PEE.5: 21 residues within 4Å: Chain C: W.30, Y.95, G.99, R.100, L.102, Y.103, Y.104, F.276, S.297, L.301, M.316, Q.322, F.325, W.326, V.329, L.332, L.333, T.336, Y.358 Chain G: V.49 Ligands: CDL.14 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:W.30, C:W.30, C:W.30, C:Y.95, C:Y.95, C:L.102, C:Y.103, C:F.276, C:L.301, C:L.301, C:F.325, C:F.325, C:W.326, C:V.329, C:L.332, C:L.333 Hydrogen bonds: C:Y.103, C:Y.104, C:Q.322 PEE.11: 15 residues within 4Å: Chain C: L.43, M.82, I.236, M.240 Chain D: H.284, R.287, M.288, K.291, M.292, M.295 Chain E: Y.127, A.128, N.131, V.132, Q.135 8 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: D:M.295, C:L.43, C:I.236, E:V.132 Hydrogen bonds: D:H.284, E:Q.135 Salt bridges: D:H.284, D:K.291

1 x HEC: HEME C(Non-covalent)

HEC.6: 23 residues within 4Å: Chain D: V.116, V.120, C.121, 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, P.247, V.270 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:V.116, D:V.120, D:V.120, D:A.192, D:P.194, D:P.195, D:L.197, D:I.200, D:V.211, D:L.214, D:L.215, D:M.244, D:V.270 Hydrogen bonds: D:Y.210, D:G.243 Salt bridges: D:R.204 Metal complexes: D:H.125

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.10: 22 residues within 4Å: Chain C: S.29, N.32, F.33, L.36, I.92, K.227, L.230, G.231, L.234, L.235 Chain D: L.300, Y.304, K.307, R.308, K.315 Chain F: R.72, Q.73 Chain G: G.34, N.37, V.38, R.41 Ligands: CDL.14 17 PLIP interactions: 6 interactions with chain C, 2 interactions with chain G, 9 interactions with chain D Hydrophobic interactions: C:N.32, C:F.33, C:L.36, C:I.92, C:L.234, D:L.300, D:Y.304, D:Y.304 Salt bridges: C:K.227, G:R.41, D:K.307, D:K.307, D:R.308, D:K.315 Hydrogen bonds: G:N.37, D:Y.304, D:K.315 CDL.14: 12 residues within 4Å: Chain C: S.28, S.29, W.30, F.33, M.96 Chain F: Q.73 Chain G: V.38, R.41, T.42, C.45 Ligands: PEE.5, CDL.10 6 PLIP interactions: 1 interactions with chain C, 4 interactions with chain G, 1 interactions with chain F Hydrogen bonds: C:S.29, F:Q.73 Hydrophobic interactions: G:T.42 Salt bridges: G:R.41, G:R.41, G:R.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Capper, M.J. et al., Antimalarial 4(1H)-Pyridones Bind to the Qi Site of Cytochrome Bc1. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-01-14

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: EI
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 9: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

I
I

F
F

G
G

H
H

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 9

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