SMTL ID : 4d6t.1 (1 other biounit)

Cytochrome bc1 bound to the 4(1H)-pyridone GW844520

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.57 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: 21 residues within 4Å: Chain C: L.41, Q.44, I.45, G.48, L.49, L.51, A.52, 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 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:L.41, C:Q.44, C:I.45, C:L.51, C:L.51, C:A.84, 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 pi-Stacking: C:H.83, C:H.83, C:H.182, C:H.182 Metal complexes: C:H.83, C:H.182 HEM.2: 19 residues within 4Å: Chain C: W.31, G.34, S.35, L.37, 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: 4X9.3 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:W.113, C:W.113, C:V.117, 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 4X9: 3-chloro-2,6-dimethyl-5-{4-[4-(trifluoromethoxy)phenoxy]phenyl}pyridin-4-ol(Non-covalent)

4X9.3: 14 residues within 4Å: Chain C: 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.2 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.18, C:F.18, C:I.42, C:L.197, C:F.220, C:F.220 pi-Stacking: C:F.220

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

PO4.4: 3 residues within 4Å: Chain A: S.473, F.476 Chain C: H.221 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Salt bridges: C:H.221 Hydrogen bonds: A:S.473 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.39 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: 1 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:S.134, C:Y.75, C:Y.75 PO4.12: 4 residues within 4Å: Chain A: F.476 Chain E: Y.115, T.118 Chain J: F.21 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: 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: 15 residues within 4Å: Chain C: W.30, Y.95, G.99, R.100, Y.103, Y.104, F.276, M.316, F.325, W.326, V.329, L.332, L.333, T.336 Ligands: CDL.14 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:W.30, C:W.30, C:Y.95, C:Y.95, C:Y.103, C:F.276, C:F.276, C:F.325, C:W.326, C:W.326, C:W.326, C:V.329, C:V.329, C:L.332, C:L.332, C:L.333 Hydrogen bonds: C:Y.103, C:Y.104, C:Q.322 PEE.11: 14 residues within 4Å: Chain C: M.82, I.236, M.240 Chain D: H.224, R.227, M.228, K.231, M.232, M.235 Chain E: Y.127, A.128, N.131, V.132, Q.135 7 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: D:M.235, C:I.236, E:V.132 Hydrogen bonds: D:H.224, E:Q.135 Salt bridges: D:H.224, D:K.231

1 x HEC: HEME C(Non-covalent)

HEC.6: 19 residues within 4Å: Chain D: V.56, V.60, C.61, C.64, H.65, N.129, A.132, P.134, P.135, L.137, I.140, R.144, Y.150, L.155, F.177, I.182, G.183, M.184, P.187 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:V.56, D:V.60, D:N.129, D:P.134, D:P.135, D:L.137, D:I.140, D:L.155, D:P.187 Hydrogen bonds: D:Y.150, D:G.183 Salt bridges: D:R.144 Metal complexes: D:H.65

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.10: 20 residues within 4Å: Chain C: S.29, N.32, F.33, L.36, M.89, K.227, L.230, G.231, L.234, L.235 Chain D: Y.244, K.247, R.248, K.255 Chain F: R.72, Q.73 Chain G: G.34, N.37, R.41 Ligands: CDL.14 14 PLIP interactions: 5 interactions with chain C, 7 interactions with chain D, 2 interactions with chain G Hydrophobic interactions: C:N.32, C:F.33, C:L.36, C:L.234, D:Y.244 Salt bridges: C:K.227, D:K.247, D:K.247, D:R.248, D:K.255 Hydrogen bonds: D:Y.244, D:K.255, G:N.37, G:R.41 CDL.14: 11 residues within 4Å: Chain C: S.28, S.29, W.30, M.96 Chain F: Q.73 Chain G: V.38, R.41, T.42, C.45 Ligands: PEE.5, CDL.10 7 PLIP interactions: 1 interactions with chain F, 2 interactions with chain C, 4 interactions with chain G Hydrogen bonds: F:Q.73, C:S.29, C:W.30 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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