SMTL ID : 4ytm.1 (1 other biounit)

Crystal structure of Mitochondrial rhodoquinol-fumarate reductase from Ascaris suum with N-biphenyl-3-yl-2-(trifluoromethyl)benzamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

MLI.1: 12 residues within 4Å: Chain A: Q.84, 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:R.320, A:A.435 Salt bridges: A:H.276, A:R.320, A:H.387, A:R.432

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

FAD.2: 36 residues within 4Å: Chain A: I.47, G.48, A.49, G.50, G.51, A.52, 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 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:L.286 Hydrogen bonds: A:A.49, A:G.51, A:A.52, A:K.72, A:K.72, A:M.73, A:S.78, A:H.79, A:T.80, A:Q.84, A:G.85, A:G.86, A:G.86, A:A.201, A:A.201, A:G.237, A:E.421, A:E.421, 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: 8 residues within 4Å: Chain B: R.87, S.88, C.89, C.94, G.95, 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: 10 residues within 4Å: Chain B: C.182, C.185, A.186, C.187, C.188, A.206, M.209, C.249, P.250, K.251 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: 10 residues within 4Å: Chain B: C.192, Y.202, C.239, H.240, T.241, 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: 20 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 Chain D: R.63, A.66, M.69, V.70, I.73, H.95, V.96, G.99, V.103 Ligands: F6A.7 16 PLIP interactions: 8 interactions with chain D, 6 interactions with chain C, 2 interactions with chain B, Hydrophobic interactions: D:A.66, D:M.69, D:V.70, D:I.73, D:V.96, D:V.103, C:M.82, C:A.83, C:T.132 Salt bridges: D:R.63, C:R.76, B:H.240 Metal complexes: D:H.95, C:H.131 pi-Stacking: C:H.75 Hydrogen bonds: B:H.240

1 x F6A: N-biphenyl-3-yl-2-(trifluoromethyl)benzamide(Non-covalent)

F6A.7: 13 residues within 4Å: Chain B: P.193, S.194, W.196, W.197, H.240 Chain C: L.60, Y.63, W.69, S.72, R.76 Chain D: D.106, Y.107 Ligands: HEM.6 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:W.196, B:W.196, B:W.197, B:H.240, C:L.60, C:L.60, C:Y.63 pi-Stacking: C:W.69 pi-Cation interactions: C:R.76

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

EPH.8: 16 residues within 4Å: Chain C: M.82, T.85, I.128, L.133, I.166, V.170 Chain D: V.70, I.73, A.76, Y.77, H.80, L.88, L.92, F.150, E.151, W.154 14 PLIP interactions: 6 interactions with chain C, 8 interactions with chain D Hydrophobic interactions: C:M.82, C:T.85, C:I.128, C:L.133, C:I.166, C:V.170, D:V.70, D:I.73, D:Y.77, D:L.88, D:L.92 Hydrogen bonds: D:Y.77 Salt bridges: D:H.80, D:H.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inaoka, D.K. et al., Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria. Int J Mol Sci (2015)

Release Date

2015-08-05

Peptides

Succinate dehydrogenase flavoprotein: 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
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Succinate dehydrogenase flavoprotein

Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

Cytochrome b-large subunit

Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial

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