SMTL ID : 7jz2.1

Succinate: quinone oxidoreductase SQR from E.coli K12

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 33 residues within 4Å: Chain A: I.13, G.14, A.15, G.16, G.17, A.18, S.37, K.38, V.39, S.44, H.45, T.46, S.48, A.49, Q.50, G.51, G.52, W.164, A.166, A.201, T.202, T.213, N.214, I.217, D.221, H.354, Y.355, G.387, E.388, G.402, S.404, L.405, L.408 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:A.15, A:G.16, A:G.17, A:A.18, A:G.19, A:K.38, A:V.39, A:S.44, A:S.44, A:S.44, A:H.45, A:T.46, A:T.46, A:Q.50, A:G.51, A:G.52, A:G.52, A:A.166, A:A.166, A:D.221, A:E.388, A:E.388, A:G.402, A:S.404, A:S.404, A:L.405 pi-Stacking: A:H.354 FAD.9: 33 residues within 4Å: Chain E: I.13, G.14, A.15, G.16, G.17, A.18, S.37, K.38, V.39, S.44, H.45, T.46, S.48, A.49, Q.50, G.51, G.52, W.164, A.166, A.201, T.202, T.213, N.214, I.217, D.221, H.354, Y.355, G.387, E.388, G.402, S.404, L.405, L.408 27 PLIP interactions: 27 interactions with chain E Hydrogen bonds: E:A.15, E:G.16, E:G.17, E:A.18, E:G.19, E:K.38, E:V.39, E:S.44, E:S.44, E:S.44, E:H.45, E:T.46, E:T.46, E:Q.50, E:G.51, E:G.52, E:G.52, E:A.166, E:A.166, E:D.221, E:E.388, E:E.388, E:G.402, E:S.404, E:S.404, E:L.405 pi-Stacking: E:H.354 FAD.17: 33 residues within 4Å: Chain I: I.13, G.14, A.15, G.16, G.17, A.18, S.37, K.38, V.39, S.44, H.45, T.46, S.48, A.49, Q.50, G.51, G.52, W.164, A.166, A.201, T.202, T.213, N.214, I.217, D.221, H.354, Y.355, G.387, E.388, G.402, S.404, L.405, L.408 27 PLIP interactions: 27 interactions with chain I Hydrogen bonds: I:A.15, I:G.16, I:G.17, I:A.18, I:G.19, I:K.38, I:V.39, I:S.44, I:S.44, I:S.44, I:H.45, I:T.46, I:T.46, I:Q.50, I:G.51, I:G.52, I:G.52, I:A.166, I:A.166, I:D.221, I:E.388, I:E.388, I:G.402, I:S.404, I:S.404, I:L.405 pi-Stacking: I:H.354

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

NA.2: 4 residues within 4Å: Chain A: M.356, M.357, G.358, E.388 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.357 NA.10: 4 residues within 4Å: Chain E: M.356, M.357, G.358, E.388 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:M.356 NA.18: 4 residues within 4Å: Chain I: M.356, M.357, G.358, E.388 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:G.358

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

FES.3: 9 residues within 4Å: Chain B: S.54, C.55, R.56, G.58, C.60, G.61, S.62, D.63, C.75 2 PLIP interactions: 2 interactions with chain B, Metal complexes: B:D.63, B:C.75 FES.11: 9 residues within 4Å: Chain F: S.54, C.55, R.56, G.58, C.60, G.61, S.62, D.63, C.75 2 PLIP interactions: 2 interactions with chain F, Metal complexes: F:D.63, F:C.75 FES.19: 9 residues within 4Å: Chain J: S.54, C.55, R.56, G.58, C.60, G.61, S.62, D.63, C.75 2 PLIP interactions: 2 interactions with chain J, Metal complexes: J:D.63, J:C.75

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

SF4.4: 9 residues within 4Å: Chain B: C.149, I.150, C.152, C.155, A.173, C.216, P.217, K.218, L.220 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.149, B:C.152, B:C.155, B:C.216 SF4.12: 9 residues within 4Å: Chain F: C.149, I.150, C.152, C.155, A.173, C.216, P.217, K.218, L.220 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.149, F:C.152, F:C.155, F:C.216 SF4.20: 9 residues within 4Å: Chain J: C.149, I.150, C.152, C.155, A.173, C.216, P.217, K.218, L.220 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.149, J:C.152, J:C.155, J:C.216

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

F3S.5: 12 residues within 4Å: Chain B: C.159, F.169, P.172, C.206, H.207, S.208, I.209, M.210, N.211, C.212, T.223, I.226 1 PLIP interactions: 1 interactions with chain B, Metal complexes: B:C.159 F3S.13: 12 residues within 4Å: Chain F: C.159, F.169, P.172, C.206, H.207, S.208, I.209, M.210, N.211, C.212, T.223, I.226 1 PLIP interactions: 1 interactions with chain F, Metal complexes: F:C.159 F3S.21: 12 residues within 4Å: Chain J: C.159, F.169, P.172, C.206, H.207, S.208, I.209, M.210, N.211, C.212, T.223, I.226 1 PLIP interactions: 1 interactions with chain J, Metal complexes: J:C.159

3 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.6: 14 residues within 4Å: Chain C: L.44, L.47, L.48, S.62, M.65, M.74, L.78, L.81, V.128 Chain D: F.37, G.41, E.42, L.43, W.48 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:L.44, C:L.47, C:L.48, C:L.48, C:L.78, C:L.81, D:F.37, D:F.37, D:W.48 Hydrogen bonds: D:G.41 3PE.15: 14 residues within 4Å: Chain G: L.44, L.47, L.48, S.62, M.65, M.74, L.78, L.81, V.128 Chain H: F.37, G.41, E.42, L.43, W.48 10 PLIP interactions: 4 interactions with chain H, 6 interactions with chain G Hydrophobic interactions: H:F.37, H:F.37, H:W.48, G:L.44, G:L.47, G:L.48, G:L.48, G:L.78, G:L.81 Hydrogen bonds: H:G.41 3PE.23: 14 residues within 4Å: Chain K: L.44, L.47, L.48, S.62, M.65, M.74, L.78, L.81, V.128 Chain L: F.37, G.41, E.42, L.43, W.48 10 PLIP interactions: 6 interactions with chain K, 4 interactions with chain L Hydrophobic interactions: K:L.44, K:L.47, K:L.48, K:L.48, K:L.78, K:L.81, L:F.37, L:F.37, L:W.48 Hydrogen bonds: L:G.41

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

HEM.7: 23 residues within 4Å: Chain B: H.207 Chain C: R.31, G.34, V.35, T.37, F.38, V.41, H.84, G.88, I.89, H.91, M.92 Chain D: V.19, A.23, L.26, T.27, I.30, I.68, H.71, A.72, G.75, M.76, V.79 22 PLIP interactions: 8 interactions with chain C, 12 interactions with chain D, 2 interactions with chain B, Hydrophobic interactions: C:T.37, C:F.38, C:V.41, D:V.19, D:A.23, D:L.26, D:L.26, D:T.27, D:I.30, D:I.68, D:A.72, D:V.79 Salt bridges: C:R.31, C:H.91, D:R.20, B:H.207, B:H.207 pi-Stacking: C:H.30, C:H.84, D:H.71 Metal complexes: C:H.84 Hydrogen bonds: D:G.75 HEM.14: 23 residues within 4Å: Chain F: H.207 Chain G: R.31, G.34, V.35, T.37, F.38, V.41, H.84, G.88, I.89, H.91, M.92 Chain H: V.19, A.23, L.26, T.27, I.30, I.68, H.71, A.72, G.75, M.76, V.79 22 PLIP interactions: 12 interactions with chain H, 2 interactions with chain F, 8 interactions with chain G, Hydrophobic interactions: H:V.19, H:A.23, H:L.26, H:L.26, H:T.27, H:I.30, H:I.68, H:A.72, H:V.79, G:T.37, G:F.38, G:V.41 Hydrogen bonds: H:G.75 Salt bridges: H:R.20, F:H.207, F:H.207, G:R.31, G:H.91 pi-Stacking: H:H.71, G:H.30, G:H.84 Metal complexes: G:H.84 HEM.22: 22 residues within 4Å: Chain J: H.207 Chain K: R.31, G.34, V.35, T.37, F.38, V.41, H.84, G.88, I.89, H.91, M.92 Chain L: V.19, A.23, L.26, T.27, I.68, H.71, A.72, G.75, M.76, V.79 21 PLIP interactions: 11 interactions with chain L, 8 interactions with chain K, 2 interactions with chain J, Hydrophobic interactions: L:V.19, L:A.23, L:L.26, L:L.26, L:T.27, L:I.68, L:A.72, L:V.79, K:T.37, K:F.38, K:V.41 Hydrogen bonds: L:G.75 Salt bridges: L:R.20, K:R.31, K:H.91, J:H.207, J:H.207 pi-Stacking: L:H.71, K:H.30, K:H.84 Metal complexes: K:H.84

3 x UQ2: UBIQUINONE-2(Non-covalent)

UQ2.8: 10 residues within 4Å: Chain B: P.160, W.164, I.209 Chain C: L.15, F.20, A.24, S.27, I.28 Chain D: V.79, Y.83 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:F.20, D:V.79, D:Y.83, D:Y.83, D:Y.83 Hydrogen bonds: D:Y.83 UQ2.16: 10 residues within 4Å: Chain F: P.160, W.164, I.209 Chain G: L.15, F.20, A.24, S.27, I.28 Chain H: V.79, Y.83 6 PLIP interactions: 5 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:V.79, H:Y.83, H:Y.83, H:Y.83, G:F.20 Hydrogen bonds: H:Y.83 UQ2.24: 10 residues within 4Å: Chain J: P.160, W.164, I.209 Chain K: L.15, F.20, A.24, S.27, I.28 Chain L: V.79, Y.83 4 PLIP interactions: 1 interactions with chain K, 3 interactions with chain L Hydrophobic interactions: K:F.20, L:V.79, L:Y.83 Hydrogen bonds: L:Y.83

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

2021-01-20

Peptides

Succinate dehydrogenase flavoprotein subunit: AEI
Succinate dehydrogenase iron-sulfur subunit: BFJ
Succinate dehydrogenase cytochrome b556 subunit: CGK
Succinate dehydrogenase hydrophobic membrane anchor subunit: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

I
I

B
B

F
F

J
J

C
C

G
G

K
K

D
D

H
H

L
L

Membrane

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

Succinate dehydrogenase iron-sulfur subunit

Succinate dehydrogenase cytochrome b556 subunit

Succinate dehydrogenase hydrophobic membrane anchor subunit

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