SMTL ID : 5zdp.2 (2 other biounits)

Crystal structure of cyanide-insensitive alternative oxidase from Trypanosoma brucei with ferulenol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

homo-dimer

Ligands

4 x FE: FE (III) ION(Non-covalent)

FE.1: 7 residues within 4Å: Chain A: E.123, E.162, H.165, E.266 Ligands: FE.2, OH.3, 9AU.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.123, A:E.123, A:E.162, A:E.266, OH.3 FE.2: 7 residues within 4Å: Chain A: E.162, E.213, E.266 Ligands: FE.1, OH.3, OXY.4, 9AU.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.162, A:E.213, A:E.213, A:E.266, OH.3 FE.6: 7 residues within 4Å: Chain B: E.123, E.162, H.165, E.266 Ligands: FE.7, OH.8, 9AU.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.123, B:E.123, B:E.162, B:E.266, OH.8 FE.7: 7 residues within 4Å: Chain B: E.162, E.213, E.266 Ligands: FE.6, OH.8, OXY.9, 9AU.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.162, B:E.213, B:E.213, B:E.266, OH.8

2 x OH: HYDROXIDE ION(Non-covalent)

OH.3: 9 residues within 4Å: Chain A: E.123, A.126, E.162, E.213, E.266 Ligands: FE.1, FE.2, OXY.4, 9AU.5 No protein-ligand interaction detected (PLIP) OH.8: 9 residues within 4Å: Chain B: E.123, A.126, E.162, E.213, E.266 Ligands: FE.6, FE.7, OXY.9, 9AU.10 No protein-ligand interaction detected (PLIP)

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.4: 6 residues within 4Å: Chain A: A.126, E.162, E.213 Ligands: FE.2, OH.3, 9AU.5 No protein-ligand interaction detected (PLIP) OXY.9: 6 residues within 4Å: Chain B: A.126, E.162, E.213 Ligands: FE.7, OH.8, 9AU.10 No protein-ligand interaction detected (PLIP)

2 x 9AU: 4-oxidanyl-3-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienyl]chromen-2-one(Non-covalent)

9AU.5: 16 residues within 4Å: Chain A: C.95, R.96, F.99, R.118, L.122, E.123, T.186, L.212, E.215, A.216, T.219, Y.220 Ligands: FE.1, FE.2, OH.3, OXY.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:R.96, A:F.99, A:L.122, A:T.186, A:E.215, A:A.216, A:Y.220 Hydrogen bonds: A:T.219 Salt bridges: A:R.96, A:R.118 9AU.10: 16 residues within 4Å: Chain B: C.95, R.96, F.99, R.118, L.122, E.123, T.186, L.212, E.215, A.216, T.219, Y.220 Ligands: FE.6, FE.7, OH.8, OXY.9 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:R.96, B:F.99, B:L.122, B:T.186, B:E.215, B:A.216, B:Y.220 Salt bridges: B:R.96, B:R.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shiba, T. et al., Insights into the ubiquinol/dioxygen binding and proton relay pathways of the alternative oxidase. Biochim Biophys Acta Bioenerg (2019)

Release Date

2019-02-27

Peptides

Alternative oxidase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

Alternative oxidase, mitochondrial

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