SMTL ID : 4pd4.1

Structural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular basis of antimalarial drug action

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.04 Å

Oligo State

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

Ligands

2 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)

UMQ.1: 17 residues within 4Å: Chain A: W.401, D.402, S.427, M.428, M.429, R.430 Chain E: Y.27, V.30, G.34, S.38, A.41 Chain I: N.13, A.14, V.15, F.16, V.17 Ligands: 3PH.2 9 PLIP interactions: 3 interactions with chain I, 4 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: I:V.17 Hydrogen bonds: I:A.14, I:V.17, A:S.427, A:M.428, A:R.430, A:R.430, E:Y.27, E:Y.27 UMQ.12: 17 residues within 4Å: Chain L: W.401, D.402, S.427, M.428, M.429, R.430 Chain P: Y.27, V.30, G.34, S.38, A.41 Chain T: N.13, A.14, V.15, F.16, V.17 Ligands: 3PH.13 9 PLIP interactions: 3 interactions with chain T, 4 interactions with chain L, 2 interactions with chain P Hydrophobic interactions: T:V.17 Hydrogen bonds: T:A.14, T:V.17, L:S.427, L:M.428, L:R.430, L:R.430, P:Y.27, P:Y.27

6 x 3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE(Non-covalent)

3PH.2: 9 residues within 4Å: Chain A: S.424, M.429 Chain C: H.222, I.226, F.227, L.230 Chain E: S.37 Ligands: UMQ.1, 3PH.11 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:I.226, C:F.227 Salt bridges: C:H.222 Hydrogen bonds: A:S.424, A:S.424, A:S.424 3PH.8: 15 residues within 4Å: Chain C: W.29, M.95, M.97, A.98, Y.102, Y.103, L.302, T.317, K.323, F.327, F.329, V.330, F.333, Y.359 Chain H: Q.54 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:W.29, C:W.29, C:L.302, C:F.329, C:F.329, C:V.330, C:F.333, C:F.333 Hydrogen bonds: C:Y.102 Salt bridges: C:K.323 3PH.11: 15 residues within 4Å: Chain C: I.42, L.81, M.237 Chain D: L.208, K.211, T.212, I.215, L.216 Chain E: G.40, A.41, S.43, T.44, T.47, F.48 Ligands: 3PH.2 10 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: E:A.41, E:T.44, E:F.48, D:T.212, D:L.216, C:I.42, C:L.81, C:L.81, C:M.237 Salt bridges: D:K.211 3PH.13: 9 residues within 4Å: Chain L: S.424, M.429 Chain N: H.222, I.226, F.227, L.230 Chain P: S.37 Ligands: UMQ.12, 3PH.22 6 PLIP interactions: 3 interactions with chain L, 3 interactions with chain N Hydrogen bonds: L:S.424, L:S.424, L:S.424 Hydrophobic interactions: N:I.226, N:F.227 Salt bridges: N:H.222 3PH.19: 15 residues within 4Å: Chain N: W.29, M.95, M.97, A.98, Y.102, Y.103, L.302, T.317, K.323, F.327, F.329, V.330, F.333, Y.359 Chain S: Q.54 10 PLIP interactions: 10 interactions with chain N Hydrophobic interactions: N:W.29, N:W.29, N:L.302, N:F.329, N:F.329, N:V.330, N:F.333, N:F.333 Hydrogen bonds: N:Y.103 Salt bridges: N:K.323 3PH.22: 15 residues within 4Å: Chain N: I.42, L.81, M.237 Chain O: L.208, K.211, T.212, I.215, L.216 Chain P: G.40, A.41, S.43, T.44, T.47, F.48 Ligands: 3PH.13 10 PLIP interactions: 4 interactions with chain N, 3 interactions with chain O, 3 interactions with chain P Hydrophobic interactions: N:I.42, N:L.81, N:L.81, N:M.237, O:T.212, O:L.216, P:A.41, P:T.44, P:F.48 Salt bridges: O:K.211

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

HEM.3: 23 residues within 4Å: Chain C: L.40, Q.43, I.44, G.47, I.48, M.50, A.51, Y.54, V.65, R.79, H.82, A.83, F.89, T.127, A.128, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187, I.190 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:L.40, C:Q.43, C:Q.43, C:I.44, C:I.48, C:A.51, C:Y.54, C:V.65, C:A.83, C:F.89, C:T.127, C:F.180, C:Y.184, C:I.190 Salt bridges: C:R.79, C:R.79 Metal complexes: C:H.82, C:H.183 HEM.4: 22 residues within 4Å: Chain C: W.30, G.33, S.34, L.36, G.37, H.96, M.97, K.99, S.105, R.110, L.113, W.114, G.117, V.118, I.120, F.121, V.194, H.197, L.201, S.206, S.207 Ligands: UQ6.7 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:L.36, C:L.113, C:L.113, C:W.114, C:V.118, C:I.120, C:F.121, C:V.194, C:V.194, C:L.201 Hydrogen bonds: C:G.33, C:S.105, C:R.110, C:S.206, C:S.207 Salt bridges: C:H.96, C:K.99 Metal complexes: C:H.96, C:H.197 HEM.9: 19 residues within 4Å: Chain D: V.39, C.40, C.43, H.44, N.108, A.111, P.113, P.114, I.119, R.123, Y.129, I.130, L.134, F.157, A.163, M.164, V.167, V.190, L.194 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:N.108, D:A.111, D:P.113, D:P.113, D:P.114, D:I.119, D:I.130, D:L.134, D:L.134, D:A.163, D:M.164, D:V.167, D:V.167, D:V.190, D:L.194 Hydrogen bonds: D:Y.129, D:A.163 Salt bridges: D:R.123 Metal complexes: D:H.44 HEM.14: 23 residues within 4Å: Chain N: L.40, Q.43, I.44, G.47, I.48, M.50, A.51, Y.54, V.65, R.79, H.82, A.83, F.89, T.127, A.128, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187, I.190 18 PLIP interactions: 18 interactions with chain N, Hydrophobic interactions: N:L.40, N:Q.43, N:Q.43, N:I.44, N:I.48, N:A.51, N:Y.54, N:V.65, N:A.83, N:F.89, N:T.127, N:F.180, N:Y.184, N:I.190 Salt bridges: N:R.79, N:R.79 Metal complexes: N:H.82, N:H.183 HEM.15: 22 residues within 4Å: Chain N: W.30, G.33, S.34, L.36, G.37, H.96, M.97, K.99, S.105, R.110, L.113, W.114, G.117, V.118, I.120, F.121, V.194, H.197, L.201, S.206, S.207 Ligands: UQ6.18 19 PLIP interactions: 19 interactions with chain N, Hydrophobic interactions: N:L.36, N:L.113, N:L.113, N:W.114, N:V.118, N:I.120, N:F.121, N:V.194, N:V.194, N:L.201 Hydrogen bonds: N:G.33, N:S.105, N:R.110, N:S.206, N:S.207 Salt bridges: N:H.96, N:K.99 Metal complexes: N:H.96, N:H.197 HEM.20: 19 residues within 4Å: Chain O: V.39, C.40, C.43, H.44, N.108, A.111, P.113, P.114, I.119, R.123, Y.129, I.130, L.134, F.157, A.163, M.164, V.167, V.190, L.194 18 PLIP interactions: 18 interactions with chain O, Hydrophobic interactions: O:N.108, O:A.111, O:P.113, O:P.113, O:P.114, O:I.119, O:I.130, O:L.134, O:L.134, O:A.163, O:M.164, O:V.167, O:V.167, O:V.190, O:L.194 Hydrogen bonds: O:A.163 Salt bridges: O:R.123 Metal complexes: O:H.44

2 x AOQ: 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione(Non-covalent)

AOQ.5: 17 residues within 4Å: Chain C: F.129, M.139, W.142, G.143, V.146, I.147, I.269, P.271, L.275, F.278, Y.279, L.282, M.295, F.296, I.299 Chain P: C.150, H.151 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.147, C:I.269, C:P.271, C:L.275, C:F.278, C:F.296 AOQ.16: 17 residues within 4Å: Chain E: C.150, H.151 Chain N: F.129, M.139, W.142, G.143, V.146, I.147, I.269, P.271, L.275, F.278, Y.279, L.282, M.295, F.296, I.299 6 PLIP interactions: 6 interactions with chain N Hydrophobic interactions: N:I.147, N:I.269, N:P.271, N:L.275, N:F.278, N:F.296

2 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.6: 8 residues within 4Å: Chain C: F.3, N.7, Y.9, L.10 Chain N: T.112, N.115, V.116, H.204 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain N Hydrophobic interactions: C:L.10, C:L.10, N:V.116 Hydrogen bonds: C:N.7, N:P.109, N:T.112, N:N.115 3PE.17: 8 residues within 4Å: Chain C: T.112, N.115, V.116, H.204 Chain N: F.3, N.7, Y.9, L.10 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain N Hydrophobic interactions: C:V.116, N:L.10, N:L.10 Hydrogen bonds: C:P.109, C:T.112, C:T.112, C:N.115, N:N.7

2 x UQ6: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL(Non-covalent)

UQ6.7: 18 residues within 4Å: Chain C: Y.16, Q.22, I.26, S.34, G.37, V.41, V.45, I.48, F.49, A.191, L.198, L.201, S.206, M.221, D.229 Chain N: L.182, L.185 Ligands: HEM.4 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain N Hydrophobic interactions: C:V.41, C:I.48, C:F.49, C:A.191, C:L.198, N:L.182, N:L.185 Hydrogen bonds: C:Q.22, C:S.206 UQ6.18: 18 residues within 4Å: Chain C: L.182, L.185 Chain N: Y.16, Q.22, I.26, S.34, G.37, V.41, V.45, I.48, F.49, A.191, L.198, L.201, S.206, M.221, D.229 Ligands: HEM.15 9 PLIP interactions: 7 interactions with chain N, 2 interactions with chain C Hydrophobic interactions: N:V.41, N:I.48, N:F.49, N:A.191, N:L.198, C:L.182, C:L.185 Hydrogen bonds: N:Q.22, N:S.206

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Covalent)

FES.10: 9 residues within 4Å: Chain E: C.129, H.131, L.132, C.134, C.148, C.150, H.151, G.152, S.153 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.129, E:H.131, E:C.148, E:H.151 FES.21: 9 residues within 4Å: Chain P: C.129, H.131, L.132, C.134, C.148, C.150, H.151, G.152, S.153 4 PLIP interactions: 4 interactions with chain P, Metal complexes: P:C.129, P:H.131, P:C.148, P:H.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Birth, D. et al., Structural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular basis of antimalarial drug action. Nat Commun (2014)

Release Date

2014-06-11

Peptides

Cytochrome b-c1 complex subunit 1, mitochondrial: AL
Cytochrome b-c1 complex subunit 2, mitochondrial: BM
Cytochrome b: CN
Cytochrome c1, heme protein, mitochondrial: DO
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EP
Cytochrome b-c1 complex subunit 6: FQ
Cytochrome b-c1 complex subunit 7: GR
Cytochrome b-c1 complex subunit 8: HS
Cytochrome b-c1 complex subunit 9: IT
Igh protein: JU
Ig kappa chain V-V region HP 124E1: KV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L
A

B
B

M
B

C
C

N
C

D
D

O
D

E
E

P
E

F
F

Q
F

G
G

R
G

H
H

S
H

I
I

T
I

J
J

U
J

K
K

V
K

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 6

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 8

Cytochrome b-c1 complex subunit 9

Igh protein

Ig kappa chain V-V region HP 124E1

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