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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

FE.1: 6 residues within 4Å: Chain A: E.123, E.162, H.165, E.266 Ligands: FE.2, OH.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.123, A:E.162, A:H.165, A:E.266, OH.3 FE.2: 6 residues within 4Å: Chain A: E.162, E.213, E.266 Ligands: FE.1, OH.3, RNB.4 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.162, A:E.213, A:E.266, H2O.1, OH.3 FE.5: 6 residues within 4Å: Chain B: E.123, E.162, H.165, E.266 Ligands: FE.6, OH.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.123, B:E.162, B:H.165, B:E.266, OH.7 FE.6: 7 residues within 4Å: Chain B: E.162, E.213, E.266, H.269 Ligands: FE.5, OH.7, RNB.8 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:E.162, B:E.213, B:E.266, H2O.3, OH.7

2 x OH: HYDROXIDE ION(Non-covalent)

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

2 x RNB: 3-chloro-5-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-4,6-dihydroxy-2-methylbenzaldehyde(Non-covalent)

RNB.4: 16 residues within 4Å: Chain A: C.95, R.96, F.99, R.118, C.119, F.121, L.122, E.123, L.212, E.213, E.215, A.216, T.219, Y.220 Ligands: FE.2, OH.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:R.96, A:R.96, A:F.99, A:F.121, A:L.122, A:L.122, A:L.212, A:E.215, A:A.216 Hydrogen bonds: A:R.118, A:T.219 Halogen bonds: A:C.119 RNB.8: 16 residues within 4Å: Chain B: V.92, C.95, R.96, F.99, R.118, C.119, L.122, E.123, L.212, E.213, E.215, A.216, T.219, Y.220 Ligands: FE.6, OH.7 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.99, B:L.122, B:L.122, B:L.212, B:E.215, B:A.216, B:Y.220 Hydrogen bonds: B:R.118, B:L.212, B:T.219, B:T.219 Halogen bonds: B:C.119

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
B

B
C

Alternative oxidase, mitochondrial

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