SMTL ID : 9ilt.1

Crystal structure of alternative complex III from Chloroflexus aurantiacus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

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

Ligands

6 x HEC: HEME C

HEC.1: 29 residues within 4Å: Chain A: R.41, P.123, F.125, V.126, L.159, Y.160, M.161, C.164, L.165, H.168, L.211, T.212, N.213, C.214, C.217, H.218 Chain B: Y.78, A.865, V.878, N.880, R.881 Chain C: W.150, H.158, M.160 Chain D: Y.82, L.84 Chain E: H.27, Y.31 Ligands: HEC.2 18 PLIP interactions: 2 interactions with chain E, 7 interactions with chain A, 4 interactions with chain C, 3 interactions with chain B, 2 interactions with chain D, Hydrogen bonds: E:Y.31, C:T.157, C:T.157, B:Y.78 Salt bridges: E:H.27, A:R.41, C:H.158 Hydrophobic interactions: A:F.125, A:V.126, A:V.126, A:M.161, A:L.165, C:W.150, B:V.878, B:R.881, D:Y.82, D:L.84 Metal complexes: A:H.218 HEC.2: 22 residues within 4Å: Chain A: V.126, F.128, I.132, H.133, K.136, I.138, T.142, W.163, C.164, C.167, H.168, I.205, M.206, Q.210, L.211, V.216, C.217 Chain B: R.942, I.943, K.946 Ligands: HEC.1, HEC.3 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:V.126, A:I.132, A:K.136, A:I.138, A:I.138, A:W.163, A:W.163, A:I.205, A:I.205, A:L.211, A:V.216, B:I.943 Hydrogen bonds: A:M.206 Salt bridges: A:K.136, B:R.942, B:K.946, B:K.946 pi-Stacking: A:F.128 Metal complexes: A:H.133, A:H.168 HEC.3: 20 residues within 4Å: Chain A: H.70, V.73, F.78, A.79, K.118, Y.120, D.121, L.122, F.128, H.130, H.133, V.134, I.138, G.139, C.140, C.143, H.144, W.163 Ligands: HEC.2, HEC.4 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:H.70, A:V.73, A:A.79, A:Y.120, A:L.122, A:F.128, A:F.128, A:F.128, A:H.133, A:V.134, A:I.138, A:W.163 Hydrogen bonds: A:A.79, A:A.79, A:Y.120 Salt bridges: A:K.118, A:K.118, A:H.130 Metal complexes: A:H.144 HEC.4: 20 residues within 4Å: Chain A: Q.49, F.53, H.55, V.59, I.64, D.65, C.66, C.69, H.70, P.82, W.116, K.118, V.119, Y.120, C.140, H.144, V.147, V.153 Ligands: HEC.3, HEC.5 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:F.53, A:F.53, A:F.53, A:V.59, A:I.64, A:W.116, A:W.116, A:H.144, A:V.147, A:V.147 Hydrogen bonds: A:V.119, A:Y.120 Salt bridges: A:H.55, A:K.118 Metal complexes: A:H.55, A:H.70 HEC.5: 19 residues within 4Å: Chain A: A.52, F.53, L.57, H.58, V.62, I.64, Y.68, T.86, C.87, C.90, H.91, I.94, K.95, L.100, L.101, V.104 Chain E: V.117, R.120 Ligands: HEC.4 14 PLIP interactions: 3 interactions with chain E, 11 interactions with chain A, Hydrophobic interactions: E:V.117, E:R.120, A:L.57, A:V.62, A:I.64, A:Y.68, A:K.95, A:L.101, A:V.104 Salt bridges: E:R.120, A:K.95, A:K.95 pi-Stacking: A:F.53 Metal complexes: A:H.58 HEC.10: 23 residues within 4Å: Chain A: T.89 Chain E: Y.102, C.103, V.105, C.106, H.107, I.123, P.125, A.126, F.128, R.132, L.133, H.140, F.141, V.144, I.145, V.149, Y.150, S.161, M.162, Y.165, I.177, I.181 17 PLIP interactions: 16 interactions with chain E, 1 interactions with chain A, Hydrophobic interactions: E:I.123, E:A.126, E:F.128, E:L.133, E:F.141, E:V.144, E:V.144, E:I.145, E:I.145, E:V.149, E:I.177, E:I.181, A:T.89 Hydrogen bonds: E:S.161 Salt bridges: E:R.132, E:H.140 Metal complexes: E:H.107

3 x SF4: IRON/SULFUR CLUSTER

SF4.6: 11 residues within 4Å: Chain B: C.794, I.795, G.796, C.797, N.798, C.800, I.829, P.847, C.972, T.974, I.977 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.794, B:C.797, B:C.800, B:C.972 SF4.7: 12 residues within 4Å: Chain B: M.787, C.804, N.808, W.826, I.827, C.931, T.932, Y.933, C.934, T.966, A.967, C.968 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.804, B:C.931, B:C.934, B:C.968 SF4.8: 13 residues within 4Å: Chain B: C.850, M.851, Q.852, C.853, A.856, P.857, C.858, N.875, C.892, P.893, Y.894, V.896, R.897 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.850, B:C.853, B:C.858, B:C.892

1 x F3S: FE3-S4 CLUSTER

F3S.9: 12 residues within 4Å: Chain B: C.862, V.864, T.867, M.877, C.882, V.883, G.884, T.885, K.886, Y.887, C.888, M.928 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.862, B:C.882, B:C.888

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, W. et al., Crystal structure of the alternative complex III from the phototrophic bacterium Chloroflexus aurantiacus. Structure (2025)

Release Date

2025-03-19

Peptides

Cytochrome c7-like domain-containing protein: A
Fe-S-cluster-containing hydrogenase components 1-like protein: B
Polysulphide reductase NrfD: C
Quinol:cytochrome c oxidoreductase membrane protein: D
Cytochrome c domain-containing protein: E
Quinol:cytochrome c oxidoreductase quinone-binding subunit 2: F
ActG: G
subunit I: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
I

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c7-like domain-containing protein

Fe-S-cluster-containing hydrogenase components 1-like protein

Polysulphide reductase NrfD

Quinol:cytochrome c oxidoreductase membrane protein

Cytochrome c domain-containing protein

Quinol:cytochrome c oxidoreductase quinone-binding subunit 2

ActG

subunit I

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