SMTL ID : 2ws3.1 (2 other biounits)

Crystal structure of the E. coli succinate:quinone oxidoreductase (SQR) SdhD Tyr83Phe mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 39 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, 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: TEO.3 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:L.252 Hydrogen bonds: A:A.15, A:A.15, A:A.18, A:K.38, A:K.38, A:V.39, A:H.45, 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:G.203, A:D.221, A:E.388, 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 NA: SODIUM ION(Non-functional Binders)

NA.2: 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 TEO: MALATE LIKE INTERMEDIATE(Non-covalent)

TEO.3: 13 residues within 4Å: Chain A: Q.50, 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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.119 Hydrogen bonds: A:Q.50, 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 FES: FE2/S2 (INORGANIC) CLUSTER(Covalent)

FES.4: 10 residues within 4Å: Chain B: S.54, C.55, R.56, G.58, V.59, C.60, G.61, S.62, D.63, C.75 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.55, B:C.60, B:D.63, B:C.75

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

SF4.5: 12 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, 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.6: 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

1 x CBE: 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE(Non-covalent)

CBE.7: 11 residues within 4Å: Chain B: P.160, S.161, W.164, H.207, I.209 Chain C: S.27, I.28, R.31 Chain D: D.82, F.83 Ligands: HEM.8 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.28, B:W.164 Hydrogen bonds: C:R.31

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

HEM.8: 24 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: V.19, R.20, A.23, L.26, T.27, I.68, H.71, A.72, G.75, M.76, Q.78, V.79 Ligands: CBE.7 19 PLIP interactions: 12 interactions with chain D, 6 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: D:V.19, D:A.23, D:L.26, D:L.26, D:I.68, D:I.68, D:A.72, C:T.37, C:V.85 Hydrogen bonds: D:G.75, D:Q.78, D:Q.78 Salt bridges: D:R.20, C:R.31, C:H.91, B:H.207 Metal complexes: D:H.71, C:H.84 pi-Stacking: C:H.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruprecht, J. et al., Succinate Dehydrogenase Activity. To be Published

Release Date

2010-08-25

Peptides

SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT: A
SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT: B
SUCCINATE DEHYDROGENASE CYTOCHROME B-556 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 B-556 SUBUNIT

SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT

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