SMTL ID : 7tce.1 (1 other biounit)

Crystal structure of delta sub IV Rhodobacter Sphaeroides bc1 with the antimalarial drug atovaquone.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.85 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

HEM.1: 31 residues within 4Å: Chain A: L.55, Q.58, I.59, G.62, I.63, L.65, A.66, Y.69, V.80, I.83, R.94, H.97, A.98, A.101, F.104, F.105, M.139, T.142, A.143, G.146, Y.147, L.149, P.150, F.195, H.198, Y.199, P.202, I.205, N.279, E.295, Y.297 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:L.55, A:Q.58, A:I.59, A:L.65, A:A.66, A:Y.69, A:A.98, A:F.104, A:A.143, A:L.149, A:Y.199, A:Y.199, A:P.202 Hydrogen bonds: A:N.279 Salt bridges: A:R.94, A:R.94 pi-Stacking: A:H.97, A:H.97, A:H.198, A:H.198 Metal complexes: A:H.97, A:H.198 HEM.2: 29 residues within 4Å: Chain A: W.45, G.48, V.49, L.51, A.52, L.55, F.104, V.108, H.111, I.112, R.114, G.115, S.120, R.125, T.128, W.129, G.132, M.133, I.135, Y.136, M.139, I.205, V.209, H.212, I.213, F.216, G.220, N.221, N.222 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:L.51, A:L.51, A:F.104, A:I.112, A:T.128, A:I.135, A:V.209, A:F.216, A:F.216 Hydrogen bonds: A:G.48, A:S.120, A:N.222 Salt bridges: A:H.111, A:R.114, A:R.125 pi-Stacking: A:H.111, A:H.111, A:H.212, A:H.212 Metal complexes: A:H.111, A:H.212 HEM.10: 30 residues within 4Å: Chain D: L.55, Q.58, I.59, G.62, I.63, L.65, A.66, Y.69, V.80, R.94, H.97, A.98, A.101, F.104, F.105, M.139, T.142, A.143, G.146, Y.147, L.149, P.150, F.195, H.198, Y.199, P.202, I.205, N.279, E.295, Y.297 21 PLIP interactions: 21 interactions with chain D, Hydrophobic interactions: D:L.55, D:Q.58, D:I.59, D:I.63, D:Y.69, D:F.104, D:F.104, D:T.142, D:L.149, D:L.149, D:Y.199, D:I.205 Hydrogen bonds: D:N.279 Salt bridges: D:R.94, D:R.94 pi-Stacking: D:H.97, D:H.97, D:H.198, D:H.198 Metal complexes: D:H.97, D:H.198 HEM.11: 30 residues within 4Å: Chain D: W.45, G.48, V.49, L.51, A.52, L.55, F.104, V.108, H.111, I.112, R.114, G.115, S.120, R.125, T.128, W.129, G.132, M.133, I.135, Y.136, M.139, I.205, V.209, H.212, I.213, F.216, T.219, G.220, N.221, N.222 26 PLIP interactions: 26 interactions with chain D, Hydrophobic interactions: D:L.51, D:L.51, D:F.104, D:I.112, D:W.129, D:W.129, D:I.135, D:Y.136, D:V.209, D:F.216, D:F.216 Hydrogen bonds: D:G.48, D:T.219, D:T.219, D:N.222 Salt bridges: D:H.111, D:R.114, D:R.125 pi-Stacking: D:H.111, D:H.111, D:H.212, D:H.212 pi-Cation interactions: D:H.111, D:R.114 Metal complexes: D:H.111, D:H.212

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

AOQ.3: 21 residues within 4Å: Chain A: Y.136, L.137, M.140, F.144, Y.147, M.154, W.157, G.158, V.161, I.162, L.165, I.292, P.294, F.298, F.301, Y.302, L.305, M.336, F.337, I.340 Chain F: H.152 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: A:F.144, A:V.161, A:I.162, A:I.292, A:P.294, A:F.337 pi-Stacking: A:F.301 Hydrogen bonds: F:H.152 AOQ.12: 22 residues within 4Å: Chain C: C.151, H.152 Chain D: Y.136, L.137, M.140, F.144, Y.147, M.154, W.157, G.158, V.161, I.162, L.165, I.292, P.294, F.298, F.301, Y.302, L.305, M.336, F.337, I.340 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.144, D:I.162, D:I.292, D:P.294, D:Y.302, D:F.337 pi-Stacking: D:Y.302

2 x 6PE: 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)

6PE.4: 11 residues within 4Å: Chain A: N.42, M.44, L.110, F.113, R.114, Y.117, Y.118, R.358, F.367, W.368, A.371 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.110, A:F.113, A:F.113, A:F.367 Hydrogen bonds: A:N.42, A:Y.117, A:Y.117, A:Y.118 Salt bridges: A:R.358 6PE.13: 11 residues within 4Å: Chain D: N.42, M.44, L.110, F.113, R.114, Y.117, Y.118, R.358, F.367, W.368, A.371 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.113, D:F.113 Hydrogen bonds: D:N.42, D:Y.117 Salt bridges: D:R.358

4 x SR: STRONTIUM ION(Non-functional Binders)

SR.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SR.8: 5 residues within 4Å: Chain B: D.8, V.9, P.10, E.14, E.129 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.8, B:V.9, B:E.14, B:E.129, B:E.129 SR.15: 1 residues within 4Å: Chain D: W.313 No protein-ligand interaction detected (PLIP) SR.17: 7 residues within 4Å: Chain E: D.8, V.9, P.10, F.11, E.14, F.110, E.129 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.8, E:V.9, E:E.14, E:E.14, E:E.129

2 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.6: 15 residues within 4Å: Chain A: V.262, A.265, I.266, F.269, M.270 Chain B: E.14, G.15, P.16, Q.120, L.121, F.122, N.123, G.124, R.226, K.227 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:G.15, B:N.123, B:K.227, A:F.269 Hydrophobic interactions: A:V.262, A:A.265, A:I.266, A:F.269 BOG.14: 16 residues within 4Å: Chain D: V.262, A.265, I.266, G.268, F.269, M.270 Chain E: F.13, E.14, G.15, P.16, Q.120, N.123, G.124, I.125, R.226, K.227 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:V.262, D:A.265, D:I.266, D:F.269 Hydrogen bonds: E:G.15, E:K.227

2 x HEC: HEME C(Covalent)

HEC.7: 26 residues within 4Å: Chain B: V.31, V.35, C.36, A.38, C.39, H.40, L.94, N.96, A.97, P.98, L.100, M.103, R.107, Y.130, I.131, V.134, L.135, F.160, I.183, A.184, M.185, P.186, P.188, L.189, V.211, L.215 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:L.94, B:P.98, B:L.100, B:L.135, B:I.183, B:A.184, B:M.185, B:P.186, B:P.188, B:L.215 Hydrogen bonds: B:Y.130, B:Y.130, B:A.184 Salt bridges: B:R.107 pi-Stacking: B:H.40, B:H.40 pi-Cation interactions: B:H.40 Metal complexes: B:H.40 HEC.16: 27 residues within 4Å: Chain E: V.31, V.35, C.36, A.38, C.39, H.40, L.94, N.96, A.97, P.98, L.100, M.103, R.107, Y.130, I.131, V.134, L.135, F.160, N.162, I.183, A.184, M.185, P.186, P.188, L.189, V.211, L.215 15 PLIP interactions: 15 interactions with chain E, Hydrophobic interactions: E:L.94, E:P.98, E:L.100, E:L.135, E:I.183, E:P.188, E:L.215 Hydrogen bonds: E:Y.130, E:Y.130, E:A.184 Salt bridges: E:R.107 pi-Stacking: E:H.40, E:H.40 pi-Cation interactions: E:H.40 Metal complexes: E:H.40

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

FES.9: 10 residues within 4Å: Chain C: C.129, H.131, L.132, G.133, C.134, C.149, C.151, H.152, S.154, P.166 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.129, C:H.131, C:C.149, C:H.152 FES.18: 10 residues within 4Å: Chain F: C.129, H.131, L.132, G.133, C.134, C.149, C.151, H.152, S.154, P.166 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.129, F:H.131, F:C.149, F:H.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esser, L. et al., Crystal structure of delta sub IV Rhodobacter Sphaeroides bc1 with the antimalarial drug atovaquone. To Be Published

Release Date

2023-01-18

Peptides

Cytochrome b: AD
Cytochrome c1: BE
Ubiquinol-cytochrome c reductase iron-sulfur subunit: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
E

B
B

E
F

C
C

F
G

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b

Cytochrome c1

Ubiquinol-cytochrome c reductase iron-sulfur subunit

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