SMTL ID : 6btm.1

Structure of Alternative Complex III from Flavobacterium johnsoniae (Wild Type)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.40 Å

Oligo State

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

Ligands

6 x HEC: HEME C(Covalent)

HEC.1: 20 residues within 4Å: Chain A: H.259, Y.260, S.261, I.264, H.265, N.269, I.271, Y.275, C.276, V.293, C.294, C.297, H.298, I.301, V.304, A.305, T.308 Chain E: L.103, K.108 Ligands: HEC.2 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain E, Hydrophobic interactions: A:Y.260, A:I.264, A:I.271, A:Y.275, A:V.304, E:L.103, E:K.108 Hydrogen bonds: A:S.261, A:S.261 Salt bridges: A:H.265, E:K.108 Metal complexes: A:H.265, A:H.298 HEC.2: 21 residues within 4Å: Chain A: Q.256, Y.260, H.262, H.265, I.271, N.272, C.273, C.276, H.277, I.288, W.347, R.349, I.350, H.351, C.372, Q.373, H.376, V.379, M.385 Ligands: HEC.1, HEC.3 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:Y.260, A:H.265, A:I.271, A:I.288, A:W.347, A:W.347, A:V.379 Hydrogen bonds: A:I.350, A:H.351 Salt bridges: A:H.351 Metal complexes: A:H.262, A:H.277 HEC.3: 16 residues within 4Å: Chain A: H.277, A.280, A.286, R.349, H.351, L.353, F.359, H.361, H.364, V.365, V.370, C.372, C.375, H.376 Ligands: HEC.2, HEC.4 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:A.280, A:H.351, A:L.353, A:F.359, A:F.359, A:V.365, A:V.370 Hydrogen bonds: A:L.353 Salt bridges: A:R.349, A:R.349 Metal complexes: A:H.361, A:H.376 HEC.4: 20 residues within 4Å: Chain A: Y.358, F.359, Q.363, H.364, A.368, C.375, W.395, C.396, C.399, H.400, T.403, V.405, Y.413, T.430, K.441, C.442 Chain B: Q.874, K.881 Ligands: HEC.3, HEC.5 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:A.368, A:W.395, A:T.403, A:V.405, A:T.430 Hydrogen bonds: A:Y.413 Metal complexes: A:H.364, A:H.400 Salt bridges: B:K.881 HEC.5: 19 residues within 4Å: Chain A: P.354, F.356, V.357, L.391, T.392, M.393, C.396, G.436, L.437, E.438, C.439, C.442, H.443 Chain B: N.808, R.809 Chain C: F.150, L.153 Chain E: Y.16 Ligands: HEC.4 10 PLIP interactions: 5 interactions with chain A, 1 interactions with chain E, 1 interactions with chain B, 3 interactions with chain C, Hydrophobic interactions: A:F.356, A:V.357, A:M.393, A:L.437, B:R.809, C:F.150, C:L.153, C:L.153 Metal complexes: A:H.443 Hydrogen bonds: E:Y.16 HEC.10: 19 residues within 4Å: Chain A: N.296 Chain E: Y.60, Y.88, C.89, C.92, H.93, F.109, G.111, V.112, P.113, Y.115, R.118, I.120, V.128, L.133, N.134, A.135, M.136, V.151 7 PLIP interactions: 7 interactions with chain E, Hydrophobic interactions: E:F.109, E:V.112, E:A.135, E:V.151 Salt bridges: E:R.118, E:R.118 Metal complexes: E:H.93

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

F3S.6: 8 residues within 4Å: Chain B: C.790, A.794, M.805, C.810, V.811, T.813, C.816, M.863 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.790, B:C.810, B:C.816

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

SF4.7: 10 residues within 4Å: Chain B: C.778, Q.779, C.781, A.784, C.786, N.803, C.820, Y.822, R.825, K.865 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.778, B:C.781, B:C.786, B:C.820

2 x DKA: DECANOIC ACID(Covalent)

DKA.8: 6 residues within 4Å: Chain B: C.1 Chain E: Y.9, Q.10 Ligands: FAW.9, DKA.11, FAW.12 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.9 DKA.11: 5 residues within 4Å: Chain A: Y.242 Chain E: C.1, Y.9 Ligands: DKA.8, FAW.12 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:Y.242 Hydrophobic interactions: E:Y.9, E:Y.9

2 x FAW: (2S)-3-hydroxypropane-1,2-diyl ditetradecanoate(Covalent)

FAW.9: 4 residues within 4Å: Chain B: C.1 Chain E: Q.10, F.12 Ligands: DKA.8 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:C.1, E:F.12 Hydrophobic interactions: E:F.12 FAW.12: 6 residues within 4Å: Chain A: F.238, V.239, Y.242 Chain E: C.1 Ligands: DKA.8, DKA.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.239, A:Y.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, C. et al., Structure of the alternative complex III in a supercomplex with cytochrome oxidase. Nature (2018)

Release Date

2018-05-09

Peptides

Alternative Complex III subunit A: A
Alternative Complex III subunit B: B
Alternative Complex III subunit C: C
Alternative Complex III subunit D: D
Alternative Complex III subunit E: E
Alternative Complex III subunit F: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Alternative Complex III subunit A

Alternative Complex III subunit B

Alternative Complex III subunit C

Alternative Complex III subunit D

Alternative Complex III subunit E

Alternative Complex III subunit F