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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 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

2 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

1 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

1 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

1 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

1 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

1 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

1 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 9 PLIP interactions: 1 interactions with chain D, 5 interactions with chain B, 3 interactions with chain C Hydrogen bonds: D:Y.83, B:W.164, C:S.27 Hydrophobic interactions: B:P.160, B:W.163, B:W.164, B:I.209, C:L.15, C:I.28

1 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

1 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

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: A
Succinate dehydrogenase iron-sulfur protein: B
Succinate dehydrogenase cytochrome b-556 subunit: C
Succinate dehydrogenase hydrophobic membrane anchor protein: 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 flavoprotein subunit

Succinate dehydrogenase iron-sulfur protein

Succinate dehydrogenase cytochrome b-556 subunit

Succinate dehydrogenase hydrophobic membrane anchor protein

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