SMTL ID : 3ae1.1

Crystal structure of porcine heart mitochondrial complex II bound with N-Phenyl-2-(trifluoromethyl)-benzamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.14 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

FAD.1: 38 residues within 4Å: Chain A: G.26, A.27, G.28, G.29, A.30, V.48, T.49, K.50, L.51, S.56, H.57, T.58, A.60, A.61, Q.62, G.63, G.64, Y.177, F.178, A.179, A.213, T.214, G.215, T.225, S.226, D.233, L.264, H.365, Y.366, G.397, E.398, R.409, A.412, N.413, S.414, L.415, L.418 Ligands: MLI.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:A.60, A:L.264 Hydrogen bonds: A:A.27, A:A.27, A:G.29, A:A.30, A:G.31, A:K.50, A:K.50, A:L.51, A:L.51, A:H.57, A:T.58, A:T.58, A:Q.62, A:G.63, A:G.64, A:G.64, A:A.179, A:G.215, A:D.233, A:E.398, A:E.398, A:R.409, A:S.414, A:S.414, A:L.415 pi-Cation interactions: A:H.365

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.2: 13 residues within 4Å: Chain A: G.63, F.131, H.254, L.264, T.266, E.267, G.268, R.298, H.365, R.409, G.411, A.412 Ligands: FAD.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.264 Hydrogen bonds: A:E.267, A:G.268, A:A.412 Salt bridges: A:H.254, A:H.254, A:R.298, A:R.298, A:H.365, A:R.409

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

FES.3: 11 residues within 4Å: Chain B: S.64, C.65, R.66, G.68, I.69, C.70, G.71, S.72, C.73, L.83, C.85 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.65, B:C.70, B:C.73, B:C.85

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

SF4.4: 13 residues within 4Å: Chain B: C.158, I.159, L.160, C.161, A.162, C.163, C.164, A.182, C.225, P.226, K.227, L.229, P.231 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.158, B:C.161, B:C.164, B:C.225

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.5: 13 residues within 4Å: Chain B: C.168, S.170, Y.178, P.181, R.214, C.215, H.216, T.217, I.218, M.219, N.220, C.221, I.235 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.168, B:C.215, B:C.221

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

HEM.6: 22 residues within 4Å: Chain B: H.216 Chain C: H.42, R.43, G.46, L.49, S.50, L.95, H.98, T.99, G.102, H.105 Chain D: R.14, S.17, L.20, L.21, L.24, L.43, H.46, G.50, I.51, V.54 Ligands: TFZ.7 17 PLIP interactions: 8 interactions with chain C, 8 interactions with chain D, 1 interactions with chain B, Hydrophobic interactions: C:R.43, C:L.49, C:L.95, C:T.99, D:L.20, D:L.20, D:L.21, D:L.24, D:L.43, D:I.51 Salt bridges: C:R.43, C:H.105, D:R.14, B:H.216 pi-Stacking: C:H.42 Metal complexes: C:H.98, D:H.46

1 x TFZ: N-phenyl-2-(trifluoromethyl)benzamide(Non-covalent)

TFZ.7: 11 residues within 4Å: Chain B: P.169, W.173, H.216, I.218 Chain C: W.32, M.36, S.39, I.40, R.43 Chain D: Y.58 Ligands: HEM.6 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:P.169, B:H.216, B:I.218, C:W.32, C:W.32, C:I.40, C:I.40, C:R.43 Hydrogen bonds: C:R.43

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

EPH.8: 10 residues within 4Å: Chain D: L.24, A.27, Y.28, P.31, L.39, C.94, V.97, A.98, W.101, K.102 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.24, D:A.27, D:Y.28, D:L.39, D:V.97, D:V.97, D:W.101 Hydrogen bonds: D:K.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harada, S. et al., Crystal structure of porcine heart mitochondrial complex II bound with N-Phenyl-2-(trifluoromethyl)-benzamide. to be published

Release Date

2011-02-09

Peptides

Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial: A
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial: B
Succinate dehydrogenase cytochrome b560 subunit, mitochondrial: C
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial: 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 [ubiquinone] flavoprotein subunit, mitochondrial

Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

Succinate dehydrogenase cytochrome b560 subunit, mitochondrial

Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial

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