SMTL ID : 6wu6.1

succinate-coenzyme Q reductase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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

FES.1: 10 residues within 4Å: Chain A: S.54, C.55, R.56, G.58, V.59, C.60, G.61, S.62, D.63, C.75 6 PLIP interactions: 6 interactions with chain A, Metal complexes: A:C.55, A:C.60, A:S.62, A:S.62, A:D.63, A:C.75 FES.5: 10 residues within 4Å: Chain D: S.54, C.55, R.56, G.58, V.59, C.60, G.61, S.62, D.63, C.75 6 PLIP interactions: 6 interactions with chain D, Metal complexes: D:C.55, D:C.60, D:S.62, D:S.62, D:D.63, D:C.75 FES.9: 10 residues within 4Å: Chain G: S.54, C.55, R.56, G.58, V.59, C.60, G.61, S.62, D.63, C.75 6 PLIP interactions: 6 interactions with chain G, Metal complexes: G:C.55, G:C.60, G:S.62, G:S.62, G:D.63, G:C.75

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

SF4.2: 11 residues within 4Å: Chain A: C.149, I.150, L.151, C.152, A.153, C.155, A.173, C.216, P.217, K.218, L.220 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.149, A:C.152, A:C.155, A:C.216 SF4.6: 11 residues within 4Å: Chain D: C.149, I.150, L.151, C.152, A.153, C.155, A.173, C.216, P.217, K.218, L.220 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.149, D:C.152, D:C.155, D:C.216 SF4.10: 11 residues within 4Å: Chain G: C.149, I.150, L.151, C.152, A.153, C.155, A.173, C.216, P.217, K.218, L.220 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.149, G:C.152, G:C.155, G:C.216

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

F3S.3: 11 residues within 4Å: Chain A: C.159, S.161, F.169, P.172, C.206, S.208, I.209, M.210, N.211, C.212, I.226 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.159, A:C.206, A:C.212 F3S.7: 11 residues within 4Å: Chain D: C.159, S.161, F.169, P.172, C.206, S.208, I.209, M.210, N.211, C.212, I.226 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.159, D:C.206, D:C.212 F3S.11: 11 residues within 4Å: Chain G: C.159, S.161, F.169, P.172, C.206, S.208, I.209, M.210, N.211, C.212, I.226 3 PLIP interactions: 3 interactions with chain G, Metal complexes: G:C.159, G:C.206, G:C.212

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

HEM.4: 16 residues within 4Å: Chain B: H.30, G.34, T.37, L.81, H.84, V.85, G.88 Chain C: A.23, L.26, T.27, I.30, I.68, H.71, G.75, Q.78, V.79 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain C, Hydrophobic interactions: B:T.37, B:L.81, B:V.85, C:A.23, C:L.26, C:I.30, C:I.68, C:V.79 Salt bridges: B:H.30, B:H.91 pi-Stacking: B:H.30, B:H.84 Metal complexes: B:H.84 HEM.8: 16 residues within 4Å: Chain E: H.30, G.34, T.37, L.81, H.84, V.85, G.88 Chain F: A.23, L.26, T.27, I.30, I.68, H.71, G.75, Q.78, V.79 13 PLIP interactions: 5 interactions with chain F, 8 interactions with chain E, Hydrophobic interactions: F:A.23, F:L.26, F:I.30, F:I.68, F:V.79, E:T.37, E:L.81, E:V.85 Salt bridges: E:H.30, E:H.91 pi-Stacking: E:H.30, E:H.84 Metal complexes: E:H.84 HEM.12: 16 residues within 4Å: Chain H: H.30, G.34, T.37, L.81, H.84, V.85, G.88 Chain I: A.23, L.26, T.27, I.30, I.68, H.71, G.75, Q.78, V.79 13 PLIP interactions: 8 interactions with chain H, 5 interactions with chain I, Hydrophobic interactions: H:T.37, H:L.81, H:V.85, I:A.23, I:L.26, I:I.30, I:I.68, I:V.79 Salt bridges: H:H.30, H:H.91 pi-Stacking: H:H.30, H:H.84 Metal complexes: H:H.84

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

FAD.13: 31 residues within 4Å: Chain J: I.13, G.14, A.15, G.16, G.17, A.18, K.38, V.39, S.44, H.45, T.46, S.48, A.49, Q.50, Y.165, T.202, I.217, T.219, D.221, H.354, Y.355, G.387, E.388, R.399, L.400, G.401, G.402, N.403, S.404, L.405, L.408 19 PLIP interactions: 19 interactions with chain J Hydrophobic interactions: J:Q.50 Hydrogen bonds: J:A.15, J:G.16, J:G.16, J:A.18, J:H.45, J:T.46, J:T.46, J:T.202, J:T.219, J:E.388, J:L.400, J:G.402, J:S.404, J:S.404, J:L.405 pi-Stacking: J:Y.165, J:H.354, J:H.354 FAD.15: 31 residues within 4Å: Chain K: I.13, G.14, A.15, G.16, G.17, A.18, K.38, V.39, S.44, H.45, T.46, S.48, A.49, Q.50, Y.165, T.202, I.217, T.219, D.221, H.354, Y.355, G.387, E.388, R.399, L.400, G.401, G.402, N.403, S.404, L.405, L.408 19 PLIP interactions: 19 interactions with chain K Hydrophobic interactions: K:Q.50 Hydrogen bonds: K:A.15, K:G.16, K:G.16, K:A.18, K:H.45, K:T.46, K:T.46, K:T.202, K:T.219, K:E.388, K:L.400, K:G.402, K:S.404, K:S.404, K:L.405 pi-Stacking: K:Y.165, K:H.354, K:H.354 FAD.17: 31 residues within 4Å: Chain L: I.13, G.14, A.15, G.16, G.17, A.18, K.38, V.39, S.44, H.45, T.46, S.48, A.49, Q.50, Y.165, T.202, I.217, T.219, D.221, H.354, Y.355, G.387, E.388, R.399, L.400, G.401, G.402, N.403, S.404, L.405, L.408 19 PLIP interactions: 19 interactions with chain L Hydrophobic interactions: L:Q.50 Hydrogen bonds: L:A.15, L:G.16, L:G.16, L:A.18, L:H.45, L:T.46, L:T.46, L:T.202, L:T.219, L:E.388, L:L.400, L:G.402, L:S.404, L:S.404, L:L.405 pi-Stacking: L:Y.165, L:H.354, L:H.354

3 x NA: SODIUM ION(Non-functional Binders)

NA.14: 5 residues within 4Å: Chain J: M.236, M.356, G.358, G.359, I.389 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:I.389 NA.16: 5 residues within 4Å: Chain K: M.236, M.356, G.358, G.359, I.389 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:M.356 NA.18: 5 residues within 4Å: Chain L: M.236, M.356, G.358, G.359, I.389 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:I.389

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, C.C. et al., A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins. Nat.Methods (2021)

Release Date

2021-02-03

Peptides

Succinate dehydrogenase iron-sulfur subunit: ADG
Succinate dehydrogenase: BEH
Succinate dehydrogenase hydrophobic membrane anchor subunit: CFI
Succinate dehydrogenase flavoprotein subunit: JKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
F

G
J

B
C

E
G

H
K

C
D

F
H

I
L

J
A

K
E

L
I

Membrane

We predict this structure to be a membrane protein.
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Succinate dehydrogenase iron-sulfur subunit

Succinate dehydrogenase

Succinate dehydrogenase hydrophobic membrane anchor subunit

Succinate dehydrogenase flavoprotein subunit

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