SMTL ID : 5kkz.1 (1 other biounit)

Rhodobacter sphaeroides bc1 with famoxadone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.97 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

HEM.1: 28 residues within 4Å: Chain A: 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, T.142, A.143, G.146, Y.147, L.149, P.150, F.195, H.198, Y.199, P.202, I.205, Y.297 Chain D: S.196 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:L.55, A:Q.58, A:I.59, A:L.65, A:A.66, A:A.101, A:F.104, A:T.142, A:L.149, A:L.149, A:Y.199, A:Y.199, A:P.202 Salt bridges: A:R.94, A:R.94 Metal complexes: A:H.97, A:H.198 HEM.2: 31 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, Y.121, 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 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:L.51, A:L.51, A:F.104, A:I.112, A:T.128, A:W.129, A:W.129, A:I.135, A:F.216, A:F.216, A:F.216 Hydrogen bonds: A:G.48, A:T.219, A:T.219, A:N.222 Salt bridges: A:H.111, A:R.114, A:R.125 Metal complexes: A:H.111, A:H.212 HEM.11: 30 residues within 4Å: Chain A: S.196 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, Y.297 16 PLIP interactions: 16 interactions with chain D, Hydrophobic interactions: D:L.55, D:Q.58, D:I.63, D:L.65, D:Y.69, D:A.101, D:F.104, D:T.142, D:L.149, D:L.149, D:Y.199, D:Y.199 Salt bridges: D:R.94, D:R.94 Metal complexes: D:H.97, D:H.198 HEM.12: 32 residues within 4Å: Chain D: W.45, W.47, G.48, V.49, L.51, A.52, L.55, F.104, V.108, H.111, I.112, R.114, G.115, S.120, Y.121, 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 24 PLIP interactions: 24 interactions with chain D, Hydrophobic interactions: D:L.51, D:L.51, D:F.104, D:V.108, D:I.112, D:T.128, D:W.129, D:W.129, D:I.135, D:Y.136, D:V.209, D:F.216, D:F.216, 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 Metal complexes: D:H.111, D:H.212

2 x FMX: FAMOXADONE(Non-covalent)

FMX.3: 21 residues within 4Å: Chain A: M.140, A.141, A.143, F.144, Y.147, M.154, S.155, G.158, V.161, I.162, L.165, F.166, I.292, V.293, P.294, E.295, Y.297, F.298, Y.302, M.336, F.337 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.144, A:F.144, A:F.144, A:Y.147, A:V.161, A:I.162, A:I.162, A:I.162, A:F.166, A:P.294, A:E.295, A:F.298 Hydrogen bonds: A:E.295 Water bridges: A:V.293, A:E.295 pi-Stacking: A:F.298 FMX.13: 20 residues within 4Å: Chain D: M.140, A.141, A.143, F.144, Y.147, M.154, G.158, V.161, I.162, L.165, F.166, I.292, V.293, P.294, E.295, Y.297, F.298, Y.302, M.336, F.337 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:F.144, D:F.144, D:Y.147, D:V.161, D:I.162, D:I.162, D:I.162, D:F.166, D:P.294, D:E.295, D:F.298, D:Y.302 Hydrogen bonds: D:E.295 Water bridges: D:V.293, D:E.295 pi-Stacking: D:F.298

2 x ASC: ASCORBIC ACID(Non-covalent)

ASC.4: 14 residues within 4Å: Chain A: A.290, H.291, I.292, V.293, Y.302, R.306, G.381, A.382, Q.383, Q.384, T.385 Chain F: P.150, C.151, H.152 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:Y.302, A:R.306, A:A.382, A:A.382, A:Q.384, F:P.150, F:C.151 Salt bridges: A:H.291 ASC.14: 13 residues within 4Å: Chain C: P.150, C.151, H.152 Chain D: A.290, H.291, I.292, V.293, Y.302, R.306, G.381, A.382, Q.383, Q.384 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:I.292, D:Y.302, D:R.306, D:A.382, D:Q.384, C:C.151 Salt bridges: D:H.291

3 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.14, B:E.129 SR.17: 5 residues within 4Å: Chain E: D.8, V.9, P.10, E.14, 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 LOP: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE(Non-covalent)

LOP.6: 26 residues within 4Å: Chain A: N.42, M.44, W.47, N.99, S.102, L.103, I.106, Y.109, L.110, F.113, R.114, Y.117, Y.118, V.259, V.262, F.263, I.266, L.274, W.296, R.358, F.367, W.368, A.371, F.374, V.375, T.378 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.103, A:I.106, A:L.110, A:L.110, A:F.113, A:F.113, A:V.262, A:F.263, A:W.368, A:F.374 Hydrogen bonds: A:N.42, A:Y.117, A:Y.118, A:Y.118, A:R.358 Salt bridges: A:R.358 LOP.15: 26 residues within 4Å: Chain D: N.42, M.44, W.47, S.102, L.103, I.106, Y.109, L.110, F.113, R.114, Y.117, Y.118, P.224, V.259, V.262, F.263, I.266, L.274, W.296, R.358, F.367, W.368, A.371, F.374, V.375, T.378 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:L.103, D:L.110, D:F.113, D:F.113, D:V.262, D:L.274, D:F.367, D:F.374, D:F.374 Hydrogen bonds: D:N.42, D:Y.117, D:Y.118, D:R.358 Salt bridges: D:R.358

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 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:P.98, B:L.100, B:L.135, B:I.183, B:A.184, B:M.185, B:P.188, B:L.189, B:L.215 Hydrogen bonds: B:Y.130, B:Y.130, B:A.184 Salt bridges: B:R.107 pi-Stacking: 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.154, F.160, I.183, A.184, M.185, P.186, P.188, L.189, V.211, L.215 13 PLIP interactions: 13 interactions with chain E, Hydrophobic interactions: E:V.35, E:P.98, E:L.135, E:I.183, E:M.185, E:P.186, E:P.188, E:L.189 Hydrogen bonds: E:Y.130, E:Y.130, E:A.184 Salt bridges: E:R.107 Metal complexes: E:H.40

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

BOG.9: 15 residues within 4Å: Chain A: V.262, A.265, I.266, F.269, M.270 Chain B: F.13, E.14, G.15, P.16, Q.120, L.121, F.122, N.123, G.124, K.227 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.265, A:I.266, A:F.269 Hydrogen bonds: B:G.15, B:G.15, B:L.121, B:K.227 BOG.18: 13 residues within 4Å: Chain D: V.262, A.265, I.266, F.269, M.270 Chain E: E.14, G.15, P.16, L.121, F.122, N.123, G.124, K.227 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.15, E:G.124, E:K.227

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

FES.10: 11 residues within 4Å: Chain C: C.129, H.131, L.132, G.133, C.134, C.149, C.151, H.152, G.153, 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.19: 11 residues within 4Å: Chain F: C.129, H.131, L.132, G.133, C.134, C.149, C.151, H.152, G.153, 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., Hydrogen Bonding to the Substrate Is Not Required for Rieske Iron-Sulfur Protein Docking to the Quinol Oxidation Site of Complex III. J.Biol.Chem. (2016)

Release Date

2016-10-12

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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