SMTL ID : 6f0k.1

Alternative complex III

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-mer

Ligands

6 x HEC: HEME C(Covalent)

HEC.1: 30 residues within 4Å: Chain A: Y.34, L.117, P.118, Y.120, A.121, S.155, M.156, C.159, L.160, H.163, T.204, N.205, C.206, A.208, C.209, H.210 Chain B: A.880, A.881, V.883, V.893, N.895, R.896 Chain C: W.148, M.156, M.158 Chain D: Y.101, L.103 Chain E: H.35, N.37 Ligands: HEC.2 16 PLIP interactions: 7 interactions with chain A, 3 interactions with chain E, 2 interactions with chain B, 1 interactions with chain D, 3 interactions with chain C, Hydrophobic interactions: A:L.117, A:P.118, A:A.121, A:M.156, A:A.208, B:R.896, B:R.896, D:Y.101, C:W.148, C:W.148, C:W.148 Hydrogen bonds: A:Y.34, E:N.37 Metal complexes: A:H.210 Salt bridges: E:H.35, E:H.35 HEC.2: 29 residues within 4Å: Chain A: L.117, H.122, F.123, S.127, H.128, N.131, V.133, C.138, L.154, W.158, C.159, C.162, H.163, P.166, Y.169, L.170, I.200, P.202, P.203, A.208, C.209 Chain B: D.792, Y.793, R.954, Q.957, R.958, N.961 Ligands: HEC.1, HEC.3 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:L.117, A:F.123, A:N.131, A:V.133, A:Y.169, A:L.170, A:I.200, A:I.200, A:P.203, A:A.208 Hydrogen bonds: A:S.127, B:N.961 pi-Stacking: A:F.123, A:H.163 Metal complexes: A:H.163 Salt bridges: B:R.958 HEC.3: 30 residues within 4Å: Chain A: C.61, H.65, V.68, K.73, A.74, N.75, I.76, K.113, V.114, H.115, H.116, L.117, F.123, H.125, H.128, V.129, V.133, G.134, C.135, T.137, C.138, H.139, L.154, W.158, I.176, T.177 Chain B: I.81 Chain E: Q.49 Ligands: HEC.2, HEC.4 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:L.117, A:F.123, A:V.133 Hydrogen bonds: A:H.115, A:L.117 Salt bridges: A:K.73, A:K.73, A:K.113, A:K.113, A:H.116 pi-Cation interactions: A:H.115 Metal complexes: A:H.139 HEC.4: 27 residues within 4Å: Chain A: Y.44, Y.48, H.50, H.53, V.54, L.59, D.60, C.61, Y.63, C.64, H.65, I.76, P.77, T.81, W.111, V.112, K.113, V.114, H.115, C.135, H.139, I.142, V.148, T.177, M.179 Ligands: HEC.3, HEC.5 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:Y.44, A:Y.48, A:Y.48, A:Y.48, A:V.54, A:L.59, A:I.76, A:I.76, A:W.111, A:W.111, A:V.114, A:H.139, A:I.142 Hydrogen bonds: A:V.114 Metal complexes: A:H.65 HEC.5: 27 residues within 4Å: Chain A: P.46, P.47, Y.48, S.49, I.52, H.53, K.56, L.57, L.59, Y.63, P.77, T.81, C.82, N.84, C.85, H.86, I.89, L.90, S.93, R.95, L.96, V.99, W.111 Chain E: V.116, I.128, Y.133 Ligands: HEC.4 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain E, Hydrophobic interactions: A:Y.48, A:Y.48, A:I.52, A:L.57, A:Y.63, A:I.89, E:Y.133 Hydrogen bonds: A:S.93, A:S.93 Salt bridges: A:K.56, A:R.95 pi-Stacking: A:Y.48, A:H.53 Metal complexes: A:H.86 HEC.10: 29 residues within 4Å: Chain A: N.84, C.85 Chain E: Y.110, Y.113, C.114, V.116, C.117, H.118, M.129, Y.135, T.136, P.137, A.138, P.139, F.141, R.145, L.146, V.149, Y.153, I.154, V.157, I.158, V.162, R.163, N.164, M.165, Y.168, I.180, V.184 14 PLIP interactions: 14 interactions with chain E, Hydrophobic interactions: E:Y.135, E:A.138, E:F.141, E:F.141, E:L.146, E:Y.153, E:I.158, E:V.162, E:N.164, E:I.180 Hydrogen bonds: E:N.164 Salt bridges: E:R.145, E:R.163 Metal complexes: E:H.118

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.6: 16 residues within 4Å: Chain B: V.876, C.877, P.878, V.879, A.881, T.882, M.892, C.897, I.898, G.899, T.900, R.901, Y.902, C.903, R.912, M.943 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.877, B:C.897, B:C.903, B:C.903

3 x SF4: IRON/SULFUR CLUSTER(Covalent)(Non-covalent)

SF4.7: 12 residues within 4Å: Chain B: C.865, M.866, H.867, C.868, A.871, P.872, C.873, N.890, C.907, Y.909, R.912, K.945 5 PLIP interactions: 5 interactions with chain B, Metal complexes: B:C.865, B:M.866, B:C.868, B:C.873, B:C.907 SF4.8: 12 residues within 4Å: Chain B: M.800, C.817, N.821, W.839, L.840, P.864, C.946, Y.948, C.949, T.974, A.975, C.976 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.817, B:C.946, B:C.949, B:C.976 SF4.9: 13 residues within 4Å: Chain B: C.807, T.808, G.809, C.810, N.811, A.812, C.813, I.842, P.862, C.980, P.981, A.982, A.984 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.807, B:C.810, B:C.813, B:C.980

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sousa, J.S. et al., Structural basis for energy transduction by respiratory alternative complex III. Nat Commun (2018)

Release Date

2018-05-09

Peptides

Cytochrome c family protein: A
Fe-S-cluster-containing hydrogenase: B
Polysulphide reductase NrfD: C
ActD: D
Quinol:cytochrome c oxidoreductase monoheme cytochrome subunit: E
ActF: F
ActH: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
H

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c family protein

Fe-S-cluster-containing hydrogenase

Polysulphide reductase NrfD

ActD

Quinol:cytochrome c oxidoreductase monoheme cytochrome subunit

ActF

ActH