SMTL ID : 5c3j.2 (1 other biounit)

Crystal structure of Mitochondrial rhodoquinol-fumarate reductase from Ascaris suum with Ubiquinone-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.1: 11 residues within 4Å: Chain A: G.85, F.153, H.276, L.286, T.288, E.289, R.320, H.387, R.432, A.435 Ligands: FAD.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.286 Hydrogen bonds: A:G.85, A:E.289, A:A.435 Salt bridges: A:H.276, A:R.320, A:R.320, A:H.387, A:R.432

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 37 residues within 4Å: Chain A: I.47, G.48, A.49, G.50, G.51, A.52, V.70, T.71, K.72, M.73, S.78, H.79, T.80, A.82, A.83, Q.84, G.85, G.86, Y.199, F.200, A.201, A.235, T.236, G.237, T.247, D.255, L.286, H.387, Y.388, G.420, E.421, R.432, A.435, N.436, S.437, L.438 Ligands: MLI.1 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:A.82, A:A.83, A:L.286 Hydrogen bonds: A:A.49, A:A.49, A:G.50, A:G.51, A:A.52, A:K.72, A:K.72, A:M.73, A:S.78, A:S.78, A:H.79, A:T.80, A:T.80, A:Q.84, A:G.85, A:G.86, A:G.86, A:A.201, A:A.201, A:E.421, A:R.432, A:R.432, A:A.435, A:S.437, A:S.437, A:L.438 pi-Cation interactions: A:H.387

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

FES.3: 10 residues within 4Å: Chain B: R.87, S.88, C.89, G.92, C.94, G.95, S.96, C.97, L.107, C.109 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.89, B:C.94, B:C.97, B:C.109

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

SF4.4: 8 residues within 4Å: Chain B: C.182, I.183, C.185, A.186, C.188, A.206, C.249, P.250 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.182, B:C.185, B:C.188, B:C.249

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

F3S.5: 12 residues within 4Å: Chain B: C.192, S.194, Y.202, C.239, H.240, T.241, I.242, M.243, N.244, C.245, A.256, I.259 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.192, B:C.239, B:C.245

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

HEM.6: 19 residues within 4Å: Chain B: H.240 Chain C: H.75, R.76, G.79, C.80, M.82, A.83, H.131, T.132, G.135, I.139 Chain D: R.63, A.66, M.69, I.73, H.95, V.96, G.99, V.103 16 PLIP interactions: 9 interactions with chain C, 6 interactions with chain D, 1 interactions with chain B, Hydrophobic interactions: C:M.82, C:A.83, C:T.132, C:I.139, D:I.73, D:V.96, D:V.103 Salt bridges: C:R.76, D:R.63, B:H.240 pi-Stacking: C:H.75, C:H.131, C:H.131, D:H.95 Metal complexes: C:H.131, D:H.95

1 x UQ1: UBIQUINONE-1(Non-covalent)

UQ1.7: 10 residues within 4Å: Chain B: S.194, W.197, I.242 Chain C: L.60, W.69, S.72, G.73, R.76 Chain D: D.106, Y.107 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.60, C:W.69, D:Y.107 Hydrogen bonds: C:R.76, D:D.106

1 x EPH: L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE(Non-covalent)

EPH.8: 14 residues within 4Å: Chain C: M.82, T.85, L.86, L.133, I.166, V.170 Chain D: V.70, I.73, A.76, Y.77, L.88, F.150, E.151, W.154 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:T.85, C:L.86, C:L.133, C:I.166, D:V.70, D:I.73 Salt bridges: D:H.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harada, S. et al., Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria. To Be Published

Release Date

2016-06-22

Peptides

Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial: A
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial: B
Cytochrome b-large subunit: C
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Membrane

We predict this structure to be a membrane protein.
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Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

Cytochrome b-large subunit

Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial

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