SMTL ID : 1nen.2 (2 other biounits)

Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 inhibitor co-crystallized at the ubiquinone binding site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x OAA: OXALOACETATE ION(Non-covalent)

OAA.1: 13 residues within 4Å: Chain A: Q.50, G.51, F.126, H.242, L.252, T.254, E.255, R.286, H.354, R.399, G.401, G.402 Ligands: FAD.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.126 Hydrogen bonds: A:G.51, A:E.255, A:R.286, A:G.402 Water bridges: A:H.242, A:R.399 Salt bridges: A:H.242, A:H.354, A:R.399 OAA.12: 13 residues within 4Å: Chain E: Q.50, G.51, F.126, H.242, L.252, T.254, E.255, R.286, H.354, R.399, G.401, G.402 Ligands: FAD.14 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:F.126 Hydrogen bonds: E:G.51, E:E.255, E:R.286, E:G.402 Water bridges: E:H.242, E:R.399 Salt bridges: E:H.242, E:H.354, E:R.399 OAA.23: 13 residues within 4Å: Chain I: Q.50, G.51, F.126, H.242, L.252, T.254, E.255, R.286, H.354, R.399, G.401, G.402 Ligands: FAD.25 10 PLIP interactions: 10 interactions with chain I Hydrophobic interactions: I:F.126 Hydrogen bonds: I:G.51, I:E.255, I:R.286, I:G.402 Water bridges: I:H.242, I:R.399 Salt bridges: I:H.242, I:H.354, I:R.399

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: Y.355, M.356, M.357, E.388, A.390 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:M.357, A:A.390 CA.4: 2 residues within 4Å: Chain B: D.187, T.190 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.187 CA.13: 5 residues within 4Å: Chain E: Y.355, M.356, M.357, E.388, A.390 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:M.357, E:A.390 CA.15: 2 residues within 4Å: Chain F: D.187, T.190 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.187 CA.24: 5 residues within 4Å: Chain I: Y.355, M.356, M.357, E.388, A.390 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:M.357, I:A.390 CA.26: 2 residues within 4Å: Chain J: D.187, T.190 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.187

3 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.3: 40 residues within 4Å: Chain A: I.13, G.14, A.15, G.16, G.17, A.18, L.36, 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, N.218, 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 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:L.252, A:L.252 Hydrogen bonds: A:A.15, A:A.15, A:G.17, A:A.18, A:G.19, 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:N.218, A:E.388, A:R.399, A:G.402, A:S.404, A:S.404, A:L.405 Water bridges: A:D.221, A:I.389 pi-Cation interactions: A:H.354 FAD.14: 40 residues within 4Å: Chain E: I.13, G.14, A.15, G.16, G.17, A.18, L.36, 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, N.218, 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.12 28 PLIP interactions: 28 interactions with chain E Hydrophobic interactions: E:L.252, E:L.252 Hydrogen bonds: E:A.15, E:A.15, E:G.17, E:A.18, E:G.19, 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:N.218, E:E.388, E:R.399, E:G.402, E:S.404, E:S.404, E:L.405 Water bridges: E:D.221, E:I.389 pi-Cation interactions: E:H.354 FAD.25: 40 residues within 4Å: Chain I: I.13, G.14, A.15, G.16, G.17, A.18, L.36, 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, N.218, 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.23 28 PLIP interactions: 28 interactions with chain I Hydrophobic interactions: I:L.252, I:L.252 Hydrogen bonds: I:A.15, I:A.15, I:G.17, I:A.18, I:G.19, 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:N.218, I:E.388, I:R.399, I:G.402, I:S.404, I:S.404, I:L.405 Water bridges: I:D.221, I:I.389 pi-Cation interactions: I:H.354

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

FES.5: 10 residues within 4Å: Chain B: 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.16: 10 residues within 4Å: Chain F: 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.27: 10 residues within 4Å: Chain J: 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)

SF4.6: 14 residues within 4Å: Chain B: F.110, C.149, I.150, L.151, C.152, A.153, C.154, C.155, A.173, L.176, 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 SF4.17: 14 residues within 4Å: Chain F: F.110, C.149, I.150, L.151, C.152, A.153, C.154, C.155, A.173, L.176, 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 SF4.28: 14 residues within 4Å: Chain J: F.110, C.149, I.150, L.151, C.152, A.153, C.154, C.155, A.173, L.176, 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.7: 11 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, I.226 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.159, B:C.206, B:C.212 F3S.18: 11 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, I.226 3 PLIP interactions: 3 interactions with chain F, Metal complexes: F:C.159, F:C.206, F:C.212 F3S.29: 11 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, I.226 3 PLIP interactions: 3 interactions with chain J, Metal complexes: J:C.159, J:C.206, J:C.212

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

HEM.8: 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, M.92 Chain D: A.23, L.26, T.27, I.68, H.71, G.75, M.76, Q.78, V.79 Ligands: CDN.10 24 PLIP interactions: 13 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, D:V.79 Water bridges: C:H.30, C:H.30 Salt bridges: C:R.31, C:H.91, 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 HEM.19: 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, M.92 Chain H: A.23, L.26, T.27, I.68, H.71, G.75, M.76, Q.78, V.79 Ligands: CDN.21 24 PLIP interactions: 2 interactions with chain F, 13 interactions with chain G, 9 interactions with chain H, Salt bridges: F:H.207, F:H.207, G:R.31, G:H.91 Hydrophobic interactions: G:T.37, G:V.85, G:I.89, G:H.91, H:A.23, H:L.26, H:L.26, H:I.68, H:V.79 Water bridges: G:H.30, G:H.30 pi-Stacking: G:H.30, G:H.84, G:H.84, H:H.71, H:H.71 pi-Cation interactions: G:H.84 Metal complexes: G:H.84, H:H.71 Hydrogen bonds: H:Q.78 HEM.30: 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, M.92 Chain L: A.23, L.26, T.27, I.68, H.71, G.75, M.76, Q.78, V.79 Ligands: CDN.32 24 PLIP interactions: 9 interactions with chain L, 13 interactions with chain K, 2 interactions with chain J, Hydrophobic interactions: L:A.23, L:L.26, L:L.26, L:I.68, L:V.79, K:T.37, K:V.85, K:I.89, K:H.91 Hydrogen bonds: L:Q.78 pi-Stacking: L:H.71, L:H.71, K:H.30, K:H.84, K:H.84 Metal complexes: L:H.71, K:H.84 Water bridges: K:H.30, K:H.30 Salt bridges: K:R.31, K:H.91, J:H.207, J:H.207 pi-Cation interactions: K:H.84

3 x DNT: 2-[1-METHYLHEXYL]-4,6-DINITROPHENOL(Non-covalent)

DNT.9: 13 residues within 4Å: Chain B: P.160, W.163, 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 8 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: B:P.160, B:W.163, B:W.164, B:I.209, C:L.15, C:I.28 Hydrogen bonds: C:S.27, D:Y.83 DNT.20: 13 residues within 4Å: Chain F: P.160, W.163, 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 9 PLIP interactions: 5 interactions with chain F, 3 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: F:P.160, F:W.163, F:W.164, F:I.209, G:L.15, G:I.28 Hydrogen bonds: F:W.164, G:S.27, H:Y.83 DNT.31: 13 residues within 4Å: Chain J: P.160, W.163, 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 9 PLIP interactions: 4 interactions with chain J, 3 interactions with chain K, 2 interactions with chain L Hydrophobic interactions: J:P.160, J:W.163, J:W.164, J:I.209, K:L.15, K:I.28 Hydrogen bonds: K:S.27, L:Y.83, L:Y.83

3 x CDN: CARDIOLIPIN(Non-covalent)

CDN.10: 27 residues within 4Å: Chain C: V.41, L.44, S.51, A.61, S.62, M.65, L.78, A.82, L.120, L.123, A.124, V.126, L.127, V.128, W.129 Chain D: Y.29, I.30, M.33, F.37, A.38, G.41, E.42, L.43, W.48, L.65, I.68 Ligands: HEM.8 20 PLIP interactions: 9 interactions with chain C, 11 interactions with chain D Hydrophobic interactions: C:V.41, C:L.44, C:L.78, C:A.82, C:L.120, C:L.123, C:L.127, D:Y.29, D:M.33, D:F.37, D:F.37, D:F.37, D:L.65, D:I.68 Hydrogen bonds: C:V.128, C:W.129, D:F.37, D:G.41, D:L.43 Water bridges: D:G.41 CDN.21: 27 residues within 4Å: Chain G: V.41, L.44, S.51, A.61, S.62, M.65, L.78, A.82, L.120, L.123, A.124, V.126, L.127, V.128, W.129 Chain H: Y.29, I.30, M.33, F.37, A.38, G.41, E.42, L.43, W.48, L.65, I.68 Ligands: HEM.19 20 PLIP interactions: 9 interactions with chain G, 11 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:L.127, H:Y.29, H:M.33, H:F.37, H:F.37, H:F.37, H:L.65, H:I.68 Hydrogen bonds: G:V.128, G:W.129, H:F.37, H:G.41, H:L.43 Water bridges: H:G.41 CDN.32: 27 residues within 4Å: Chain K: V.41, L.44, S.51, A.61, S.62, M.65, L.78, A.82, L.120, L.123, A.124, V.126, L.127, V.128, W.129 Chain L: Y.29, I.30, M.33, F.37, A.38, G.41, E.42, L.43, W.48, L.65, I.68 Ligands: HEM.30 20 PLIP interactions: 9 interactions with chain K, 11 interactions with chain L Hydrophobic interactions: K:V.41, K:L.44, K:L.78, K:A.82, K:L.120, K:L.123, K:L.127, L:Y.29, L:M.33, L:F.37, L:F.37, L:F.37, L:L.65, L:I.68 Hydrogen bonds: K:V.128, K:W.129, L:F.37, L:G.41, L:L.43 Water bridges: L:G.41

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

EPH.11: 5 residues within 4Å: Chain C: I.22, K.107, K.111, F.114, V.118 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.114, C:F.114, C:F.114, C:V.118 Hydrogen bonds: C:K.111 Salt bridges: C:K.107, C:K.111 EPH.22: 5 residues within 4Å: Chain G: I.22, K.107, K.111, F.114, V.118 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:F.114, G:F.114, G:F.114, G:V.118 Hydrogen bonds: G:K.111 Salt bridges: G:K.107, G:K.111 EPH.33: 5 residues within 4Å: Chain K: I.22, K.107, K.111, F.114, V.118 7 PLIP interactions: 7 interactions with chain K Hydrophobic interactions: K:F.114, K:F.114, K:F.114, K:V.118 Hydrogen bonds: K:K.111 Salt bridges: K:K.107, K:K.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yankovskaya, V. et al., Architecture of succinate dehydrogenase and reactive oxygen species generation. Science (2003)

Release Date

2003-02-25

Peptides

Succinate dehydrogenase flavoprotein subunit: AEI
Succinate dehydrogenase iron-sulfur protein: BFJ
Succinate dehydrogenase cytochrome b-556 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 b-556 subunit

Succinate dehydrogenase hydrophobic membrane anchor protein

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