SMTL ID : 2acz.1

Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 inhibitor co-crystallized at the ubiquinone binding site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x OAA: OXALOACETATE ION(Non-covalent)

OAA.1: 15 residues within 4Å: Chain A: Q.50, G.51, F.126, Q.240, H.242, L.252, T.254, E.255, G.256, R.286, H.354, R.399, G.401, G.402 Ligands: FAD.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.126 Hydrogen bonds: A:G.51, A:E.255, A:G.256, A:G.402 Salt bridges: A:H.242, A:H.242, A:R.286, A:H.354, A:R.399 OAA.9: 15 residues within 4Å: Chain E: Q.50, G.51, F.126, Q.240, H.242, L.252, T.254, E.255, G.256, R.286, H.354, R.399, G.401, G.402 Ligands: FAD.10 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:F.126 Hydrogen bonds: E:G.51, E:E.255, E:G.256, E:G.402 Salt bridges: E:H.242, E:H.242, E:R.286, E:H.354, E:R.399 OAA.17: 15 residues within 4Å: Chain I: Q.50, G.51, F.126, Q.240, H.242, L.252, T.254, E.255, G.256, R.286, H.354, R.399, G.401, G.402 Ligands: FAD.18 10 PLIP interactions: 10 interactions with chain I Hydrophobic interactions: I:F.126 Hydrogen bonds: I:G.51, I:E.255, I:G.256, I:G.402 Salt bridges: I:H.242, I:H.242, I:R.286, I:H.354, I:R.399

3 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.2: 37 residues within 4Å: Chain A: 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, Y.165, A.166, A.201, T.202, G.203, T.213, N.214, D.221, L.252, H.354, Y.355, G.387, E.388, R.399, G.402, N.403, S.404, L.405, L.408 Ligands: OAA.1 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.252 Hydrogen bonds: A:A.15, A:A.15, A:G.16, A:A.18, A:K.38, A:K.38, A:V.39, A:H.45, A:T.46, A:T.46, A:Q.50, A:G.52, A:G.52, A:A.166, A:A.166, A:G.203, A:E.388, A:R.399, A:G.402, A:S.404, A:L.405 pi-Cation interactions: A:H.354 FAD.10: 37 residues within 4Å: Chain E: 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, Y.165, A.166, A.201, T.202, G.203, T.213, N.214, D.221, L.252, H.354, Y.355, G.387, E.388, R.399, G.402, N.403, S.404, L.405, L.408 Ligands: OAA.9 23 PLIP interactions: 23 interactions with chain E Hydrophobic interactions: E:L.252 Hydrogen bonds: E:A.15, E:A.15, E:G.16, E:A.18, E:K.38, E:K.38, E:V.39, E:H.45, E:T.46, E:T.46, E:Q.50, E:G.52, E:G.52, E:A.166, E:A.166, E:G.203, E:E.388, E:R.399, E:G.402, E:S.404, E:L.405 pi-Cation interactions: E:H.354 FAD.18: 37 residues within 4Å: Chain I: 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, Y.165, A.166, A.201, T.202, G.203, T.213, N.214, D.221, L.252, H.354, Y.355, G.387, E.388, R.399, G.402, N.403, S.404, L.405, L.408 Ligands: OAA.17 23 PLIP interactions: 23 interactions with chain I Hydrophobic interactions: I:L.252 Hydrogen bonds: I:A.15, I:A.15, I:G.16, I:A.18, I:K.38, I:K.38, I:V.39, I:H.45, I:T.46, I:T.46, I:Q.50, I:G.52, I:G.52, I:A.166, I:A.166, I:G.203, I:E.388, I:R.399, I:G.402, I:S.404, I:L.405 pi-Cation interactions: I:H.354

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

FES.3: 11 residues within 4Å: Chain B: R.53, S.54, C.55, R.56, G.58, V.59, C.60, G.61, D.63, L.73, C.75 5 PLIP interactions: 5 interactions with chain B, Metal complexes: B:C.55, B:C.60, B:D.63, B:D.63, B:C.75 FES.11: 11 residues within 4Å: Chain F: R.53, S.54, C.55, R.56, G.58, V.59, C.60, G.61, D.63, L.73, C.75 5 PLIP interactions: 5 interactions with chain F, Metal complexes: F:C.55, F:C.60, F:D.63, F:D.63, F:C.75 FES.19: 11 residues within 4Å: Chain J: R.53, S.54, C.55, R.56, G.58, V.59, C.60, G.61, D.63, L.73, C.75 5 PLIP interactions: 5 interactions with chain J, Metal complexes: J:C.55, J:C.60, J:D.63, J:D.63, J:C.75

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

SF4.4: 11 residues within 4Å: Chain B: C.149, I.150, C.152, A.153, C.154, 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: 11 residues within 4Å: Chain F: C.149, I.150, C.152, A.153, C.154, 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: 11 residues within 4Å: Chain J: C.149, I.150, C.152, A.153, C.154, 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: 10 residues within 4Å: Chain B: C.159, P.172, C.206, H.207, S.208, I.209, M.210, N.211, C.212, T.223 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.159, B:C.206, B:C.212 F3S.13: 10 residues within 4Å: Chain F: C.159, P.172, C.206, H.207, S.208, I.209, M.210, N.211, C.212, T.223 3 PLIP interactions: 3 interactions with chain F, Metal complexes: F:C.159, F:C.206, F:C.212 F3S.21: 10 residues within 4Å: Chain J: C.159, P.172, C.206, H.207, S.208, I.209, M.210, N.211, C.212, T.223 3 PLIP interactions: 3 interactions with chain J, Metal complexes: J:C.159, J:C.206, J:C.212

3 x HEB: HEME B/C(Non-covalent)

HEB.6: 22 residues within 4Å: Chain B: H.207 Chain C: H.30, R.31, G.34, T.37, F.38, H.84, V.85, G.88, I.89, H.91 Chain D: R.20, A.23, L.26, T.27, I.68, H.71, G.75, M.76, Q.78 Ligands: AT5.7, CDN.8 22 PLIP interactions: 11 interactions with chain C, 9 interactions with chain D, 2 interactions with chain B, Hydrophobic interactions: C:T.37, C:V.85, C:I.89, C:H.91, D:A.23, D:L.26, D:L.26, D:I.68 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, C:H.84, D:H.71, D:H.71 pi-Cation interactions: C:H.84 Metal complexes: C:H.84, D:H.71 Hydrogen bonds: D:Q.78 HEB.14: 22 residues within 4Å: Chain F: H.207 Chain G: H.30, R.31, G.34, T.37, F.38, H.84, V.85, G.88, I.89, H.91 Chain H: R.20, A.23, L.26, T.27, I.68, H.71, G.75, M.76, Q.78 Ligands: AT5.15, CDN.16 22 PLIP interactions: 9 interactions with chain H, 2 interactions with chain F, 11 interactions with chain G, Hydrophobic interactions: H:A.23, H:L.26, H:L.26, H:I.68, G:T.37, G:V.85, G:I.89, G:H.91 Hydrogen bonds: H:Q.78 Salt bridges: H:R.20, F:H.207, F:H.207, G:R.31, G:H.91 pi-Stacking: H:H.71, H:H.71, G:H.30, G:H.84, G:H.84 Metal complexes: H:H.71, G:H.84 pi-Cation interactions: G:H.84 HEB.22: 22 residues within 4Å: Chain J: H.207 Chain K: H.30, R.31, G.34, T.37, F.38, H.84, V.85, G.88, I.89, H.91 Chain L: R.20, A.23, L.26, T.27, I.68, H.71, G.75, M.76, Q.78 Ligands: AT5.23, CDN.24 22 PLIP interactions: 11 interactions with chain K, 9 interactions with chain L, 2 interactions with chain J, Hydrophobic interactions: K:T.37, K:V.85, K:I.89, K:H.91, L:A.23, L:L.26, L:L.26, L:I.68 Salt bridges: K:R.31, K:H.91, L:R.20, J:H.207, J:H.207 pi-Stacking: K:H.30, K:H.84, K:H.84, L:H.71, L:H.71 pi-Cation interactions: K:H.84 Metal complexes: K:H.84, L:H.71 Hydrogen bonds: L:Q.78

3 x AT5: 3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIMETHYL-1-OXOHEXYL]-4-HYDROXY-5,6-DIMETHOXY-2(1H)-PYRIDINONE(Non-covalent)

AT5.7: 14 residues within 4Å: Chain B: P.160, S.161, W.164, H.207, I.209 Chain C: L.15, F.20, A.24, S.27, I.28, R.31 Chain D: D.82, Y.83 Ligands: HEB.6 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.15, C:F.20, C:I.28, B:P.160 Hydrogen bonds: C:S.27, C:I.28 AT5.15: 14 residues within 4Å: Chain F: P.160, S.161, W.164, H.207, I.209 Chain G: L.15, F.20, A.24, S.27, I.28, R.31 Chain H: D.82, Y.83 Ligands: HEB.14 6 PLIP interactions: 5 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:L.15, G:F.20, G:I.28, F:P.160 Hydrogen bonds: G:S.27, G:I.28 AT5.23: 14 residues within 4Å: Chain J: P.160, S.161, W.164, H.207, I.209 Chain K: L.15, F.20, A.24, S.27, I.28, R.31 Chain L: D.82, Y.83 Ligands: HEB.22 6 PLIP interactions: 5 interactions with chain K, 1 interactions with chain J Hydrophobic interactions: K:L.15, K:F.20, K:I.28, J:P.160 Hydrogen bonds: K:S.27, K:I.28

3 x CDN: CARDIOLIPIN(Non-covalent)

CDN.8: 25 residues within 4Å: Chain C: V.41, L.44, S.51, A.61, S.62, M.65, M.74, L.78, A.82, L.120, L.123, A.124, V.126, L.127, V.128, W.129 Chain D: I.30, F.37, G.41, E.42, L.43, W.48, L.65, I.68 Ligands: HEB.6 16 PLIP interactions: 6 interactions with chain D, 10 interactions with chain C Hydrophobic interactions: D:I.30, D:F.37, D:W.48, D:L.65, D:I.68, C:V.41, C:L.44, C:L.78, C:A.82, C:L.120, C:L.123, C:A.124, C:L.127, C:L.127 Hydrogen bonds: D:L.43, C:V.128 CDN.16: 25 residues within 4Å: Chain G: V.41, L.44, S.51, A.61, S.62, M.65, M.74, L.78, A.82, L.120, L.123, A.124, V.126, L.127, V.128, W.129 Chain H: I.30, F.37, G.41, E.42, L.43, W.48, L.65, I.68 Ligands: HEB.14 16 PLIP interactions: 10 interactions with chain G, 6 interactions with chain H Hydrophobic interactions: G:V.41, G:L.44, G:L.78, G:A.82, G:L.120, G:L.123, G:A.124, G:L.127, G:L.127, H:I.30, H:F.37, H:W.48, H:L.65, H:I.68 Hydrogen bonds: G:V.128, H:L.43 CDN.24: 25 residues within 4Å: Chain K: V.41, L.44, S.51, A.61, S.62, M.65, M.74, L.78, A.82, L.120, L.123, A.124, V.126, L.127, V.128, W.129 Chain L: I.30, F.37, G.41, E.42, L.43, W.48, L.65, I.68 Ligands: HEB.22 16 PLIP interactions: 6 interactions with chain L, 10 interactions with chain K Hydrophobic interactions: L:I.30, L:F.37, L:W.48, L:L.65, L:I.68, K:V.41, K:L.44, K:L.78, K:A.82, K:L.120, K:L.123, K:A.124, K:L.127, K:L.127 Hydrogen bonds: L:L.43, K:V.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horsefield, R. et al., Structural and computational analysis of the quinone-binding site of complex II (succinate-ubiquinone oxidoreductase): a mechanism of electron transfer and proton conduction during ubiquinone reduction. J.Biol.Chem. (2006)

Release Date

2006-01-03

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

B
B

F
B

J
B

C
C

G
C

K
C

D
D

H
D

L
D

Membrane

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

Succinate dehydrogenase iron-sulfur protein

Succinate dehydrogenase cytochrome b556 subunit

Succinate dehydrogenase hydrophobic membrane anchor protein

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