SMTL ID : 9kq3.1

Cryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respiratory Complex II in pydiflumetofen-bound state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 33 residues within 4Å: Chain A: G.15, A.16, G.17, G.18, A.19, I.37, S.38, K.39, L.40, S.45, H.46, T.47, A.49, A.50, Q.51, G.52, Y.166, F.167, A.168, A.202, T.203, T.214, D.222, L.253, Y.355, G.388, E.389, R.400, A.403, N.404, S.405, L.406, L.409 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.253 Hydrogen bonds: A:G.18, A:A.19, A:K.39, A:K.39, A:L.40, A:S.45, A:H.46, A:T.47, A:Q.51, A:G.52, A:A.168, A:A.168, A:E.389, A:R.400, A:S.405, A:S.405, A:L.406 pi-Cation interactions: A:H.354

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

FES.2: 9 residues within 4Å: Chain B: S.57, C.58, R.59, G.61, I.62, C.63, G.64, C.66, C.78 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.58, B:C.63, B:C.66, B:C.78

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

SF4.3: 10 residues within 4Å: Chain B: C.150, I.151, L.152, C.153, A.154, C.156, A.174, M.177, C.217, K.219 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.150, B:C.153, B:C.156, B:C.217

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

F3S.4: 10 residues within 4Å: Chain B: C.160, Y.170, P.173, C.207, H.208, T.209, I.210, M.211, N.212, C.213 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.160, B:C.207, B:C.213

1 x 01: Pydiflumetofen

01.5: 11 residues within 4Å: Chain B: P.161, S.162, W.165, H.208, I.210 Chain C: S.38, S.39, R.42, I.43 Chain D: D.83, Y.84 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D pi-Cation interactions: C:R.42 Halogen bonds: C:S.39, D:D.83

1 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.6: 21 residues within 4Å: Chain C: L.45, M.48, G.51, F.52, F.55, F.94, F.98, H.101, Y.139, L.140 Chain D: A.50, M.51, L.52, T.53, T.54, L.69, C.73, V.123, V.126, K.127, D.131 17 PLIP interactions: 10 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:L.45, C:F.52, C:F.55, C:F.55, C:F.94, C:F.98, C:F.98, C:L.140, D:L.69, D:L.69, D:V.123, D:V.126, D:D.131 Hydrogen bonds: C:Y.139, C:Y.139 Salt bridges: D:K.127, D:K.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Z.W. et al., Cryo-EM structure of the yeast Saccharomyces cerevisiae SDH provides a template for eco-friendly fungicide discovery. Nat Commun (2025)

Release Date

2025-09-03

Peptides

Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial: A
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial: B
Sdh3p: 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 [ubiquinone] flavoprotein subunit, mitochondrial

Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

Sdh3p

Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial

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