SMTL ID : 4d6t.2 (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-1-1-1-1-1-1-1-1-1-1-mer

Ligands

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

PO4.1: 4 residues within 4Å: Chain A: F.476 Chain E: Y.115, T.118 Chain J: F.21 No protein-ligand interaction detected (PLIP) PO4.2: 3 residues within 4Å: Chain A: S.473, F.476 Chain C: H.221 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.473 Salt bridges: A:R.479 PO4.10: 2 residues within 4Å: Chain E: S.138 Ligands: PO4.11 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.138 PO4.11: 2 residues within 4Å: Chain E: S.134 Ligands: PO4.10 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.134 PO4.14: 2 residues within 4Å: Chain F: P.52, Y.94 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.94, F:Y.94

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

HEM.3: 24 residues within 4Å: Chain C: L.41, Q.44, I.45, G.48, L.49, L.51, A.52, Y.55, V.66, R.80, H.83, A.84, A.87, F.90, 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:Y.55, C:F.90, C:T.126, C:A.127, 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.4: 22 residues within 4Å: Chain C: W.31, G.34, S.35, L.37, G.38, F.90, L.94, H.97, V.98, R.100, S.106, F.109, W.113, G.116, V.117, L.120, H.196, L.197, L.200, S.205, N.206 Ligands: 4X9.5 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:F.90, C:L.94, C:V.98, C:L.120, C:L.197 Hydrogen bonds: C:G.34, C:S.106, C:S.205, 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)

4X9.5: 16 residues within 4Å: Chain C: F.18, L.21, I.27, W.31, S.35, G.38, L.41, M.190, A.193, M.194, L.197, H.201, S.205, F.220, D.228 Ligands: HEM.4 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.197

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

PEE.6: 20 residues within 4Å: Chain C: W.30, Y.95, G.99, R.100, L.102, Y.103, Y.104, F.276, M.316, Q.322, F.325, W.326, V.329, L.332, L.333, T.336 Chain F: S.70, Q.73 Chain G: V.49 Ligands: CDL.15 21 PLIP interactions: 19 interactions with chain C, 2 interactions with chain F 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:F.276, C:F.325, C:W.326, C:W.326, C:W.326, C:V.329, C:V.329, C:L.333 Hydrogen bonds: C:Y.104, C:Y.104, C:Q.322, F:Q.73, F:Q.73 PEE.9: 19 residues within 4Å: Chain C: I.39, L.43, M.82, I.229, I.236, M.240 Chain D: H.224, M.228, K.231, M.232, M.235, M.236 Chain E: Y.127, A.128, N.131, V.132, V.133, Q.135 Chain J: D.37 10 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C, 3 interactions with chain E Hydrophobic interactions: D:M.235, C:I.39, C:L.43, C:I.229, C:I.236, E:V.132, E:V.132, E:V.133 Salt bridges: D:H.224, D:K.231

1 x HEC: HEME C(Non-covalent)

HEC.7: 17 residues within 4Å: Chain D: V.56, V.60, C.61, C.64, H.65, N.129, P.134, P.135, I.140, R.144, Y.150, L.155, F.177, G.183, M.184, P.187, V.210 16 PLIP interactions: 16 interactions with chain D, Hydrophobic interactions: D:V.56, D:V.60, D:N.129, D:P.135, D:I.140, D:L.155, D:M.184, D:P.187, D:V.210 Hydrogen bonds: D:Y.150, D:Y.150, D:G.183 Salt bridges: D:R.144 pi-Stacking: D:H.65 pi-Cation interactions: D:H.65 Metal complexes: D:H.65

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.8: 17 residues within 4Å: Chain C: S.29, N.32, L.36, I.92, K.227, 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.15 15 PLIP interactions: 2 interactions with chain G, 7 interactions with chain C, 6 interactions with chain D Hydrogen bonds: G:N.37, G:R.41, D:Y.244, D:K.255 Hydrophobic interactions: C:N.32, C:L.36, C:I.92, C:L.234, C:L.234, C:L.235 Salt bridges: C:K.227, D:K.247, D:K.247, D:R.248, D:K.255 CDL.15: 10 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 Ligands: PEE.6, CDL.8 7 PLIP interactions: 2 interactions with chain C, 4 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: C:W.30, G:T.42 Hydrogen bonds: C:S.29, F:Q.73 Salt bridges: G:R.41, G:R.41, G:R.41

1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.12: 9 residues within 4Å: Chain E: C.217, H.219, L.220, C.222, C.236, H.239, G.240, S.241, P.253 1 PLIP interactions: 1 interactions with chain E, Metal complexes: E:C.236

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 3 residues within 4Å: Chain E: R.170, K.172, I.214 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.170

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: E
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 RIESKE, MITOCHONDRIAL: I
CYTOCHROME B-C1 COMPLEX SUBUNIT 9: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

B
O

C
P

D
Q

E
R

F
S

G
T

H
U

I
V

J
W

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 RIESKE, MITOCHONDRIAL

CYTOCHROME B-C1 COMPLEX SUBUNIT 9

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