SMTL ID : 4ytp.1

CRYSTAL STRUCTURE OF PORCINE HEART MITOCHONDRIAL COMPLEX II BOUND WITH N-[(4-tert-butylphenyl)methyl]-2-(trifluoromethyl)benzamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

FAD.1: 36 residues within 4Å: Chain A: V.67, G.68, A.69, G.70, G.71, A.72, V.90, T.91, K.92, L.93, S.98, H.99, T.100, A.103, Q.104, G.105, G.106, Y.219, F.220, A.221, A.255, T.256, G.257, T.267, D.275, L.306, H.407, Y.408, G.439, E.440, R.451, A.454, N.455, S.456, L.457, L.460 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:L.306, A:L.306 Hydrogen bonds: A:A.69, A:A.69, A:A.72, A:G.73, A:T.91, A:K.92, A:K.92, A:L.93, A:S.98, A:H.99, A:T.100, A:Q.104, A:G.105, A:G.106, A:G.106, A:A.221, A:A.221, A:G.257, A:D.275, A:C.438, A:E.440, A:R.451, A:A.454, A:S.456, A:S.456, A:L.457 pi-Cation interactions: A:H.407

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

FES.2: 12 residues within 4Å: Chain B: R.91, S.92, C.93, R.94, G.96, I.97, C.98, G.99, S.100, C.101, L.111, C.113 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.93, B:C.98, B:C.101, B:C.113

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

SF4.3: 10 residues within 4Å: Chain B: C.186, I.187, L.188, C.189, A.190, C.192, A.210, C.253, P.254, L.257 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.186, B:C.189, B:C.192, B:C.253

1 x F3S: FE3-S4 CLUSTER(Covalent)

F3S.4: 11 residues within 4Å: Chain B: C.196, S.198, Y.206, C.243, H.244, T.245, I.246, M.247, N.248, C.249, G.260 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.196, B:C.243, B:C.249

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

HEM.5: 20 residues within 4Å: Chain B: H.244 Chain C: H.71, R.72, G.75, I.76, L.78, S.79, V.82, H.127, T.128, G.131, H.134 Chain D: R.70, S.73, L.76, L.77, L.80, H.102, G.106, I.107 14 PLIP interactions: 8 interactions with chain C, 6 interactions with chain D, Hydrophobic interactions: C:L.78, C:L.78, C:V.82, C:T.128, D:L.76, D:L.76, D:L.80, D:I.107 Salt bridges: C:R.72, C:H.134, D:R.70 pi-Stacking: C:H.71 Metal complexes: C:H.127, D:H.102

1 x E23: N-(4-tert-butylbenzyl)-2-(trifluoromethyl)benzamide(Non-covalent)

E23.6: 12 residues within 4Å: Chain B: P.197, S.198, W.201, H.244, I.246 Chain C: I.56, W.61, S.68, I.69, R.72 Chain D: D.113, Y.114 6 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: C:I.56, C:W.61, C:I.69, C:R.72 Halogen bonds: B:S.198 Hydrogen bonds: D:Y.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inaoka, D.K. et al., Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria. Int J Mol Sci (2015)

Release Date

2015-08-05

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.
Show / Hide

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

Related Entries With Identical Sequence