SMTL ID : 2wdr.3 (2 other biounits)

E. coli succinate:quinone oxidoreductase (SQR) with pentachlorophenol bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-oligomer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 38 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, 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: TEO.2 25 PLIP interactions: 25 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: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:D.221, A:E.388, A:R.399, A:R.399, A:G.402, A:S.404, A:S.404, A:L.405 pi-Cation interactions: A:H.354

1 x TEO: MALATE LIKE INTERMEDIATE(Non-covalent)

TEO.2: 12 residues within 4Å: Chain A: G.51, F.119, H.242, L.252, T.254, E.255, R.286, H.354, R.399, G.401, G.402 Ligands: FAD.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.119 Hydrogen bonds: A:G.51, A:T.254, A:E.255, A:R.286, A:R.286, A:G.402 Salt bridges: A:H.242, A:R.286, A:R.286, A:H.354, A:R.399

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

NA.3: 6 residues within 4Å: Chain A: Y.355, M.356, M.357, G.358, E.388, A.390 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.355, A:G.358

1 x FES: FE2/S2 (INORGANIC) CLUSTER(Covalent)

FES.4: 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

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

SF4.5: 11 residues within 4Å: Chain B: C.149, I.150, L.151, C.152, A.153, C.154, C.155, A.173, C.216, P.217, 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.6: 10 residues within 4Å: Chain B: C.159, P.172, C.206, H.207, S.208, I.209, M.210, 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.7: 21 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, M.92 Chain D: R.20, A.23, L.26, T.27, I.68, H.71, A.72, G.75, M.76, Q.78 17 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B, 9 interactions with chain D, Hydrophobic interactions: C:T.37, C:I.89, D:A.23, D:L.26, D:L.26, D:I.68, D:A.72 Salt bridges: C:R.31, C:H.91, B:H.207, B:H.207, D:R.20 pi-Stacking: C:H.30 Metal complexes: C:H.84, D:H.71 Hydrogen bonds: D:Q.78, D:Q.78

1 x PCI: PENTACHLOROPHENOL(Non-covalent)

PCI.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, R.31 Chain D: Y.83 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:Y.83, B:W.164 Halogen bonds: C:A.24, C:S.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruprecht, J. et al., Structure of Escherichia Coli Succinate:Quinone Oxidoreductase with an Occupied and Empty Quinone- Binding Site. J.Biol.Chem. (2009)

Release Date

2009-08-25

Peptides

SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT: A
SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT: B
SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT: C
SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

C
K

D
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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