SMTL ID : 5k3i.4 (3 other biounits)

Crystal structure of Acyl-CoA oxidase-1 in Caenorhabditis elegans complexed with FAD and ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 27 residues within 4Å: Chain A: L.115, Y.149, Q.151, T.152, G.157, T.158, W.189, P.190, G.191, T.432, Y.433, E.436, M.438, V.439, L.442 Chain B: R.320, Q.322, V.334, Y.337, T.339, Q.340, R.343, A.408, C.409, G.410, G.411, Y.414 22 PLIP interactions: 13 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:W.189, A:Y.433, A:Y.433, B:Y.414, B:Y.414 Hydrogen bonds: A:Y.149, A:Q.151, A:T.152, A:T.152, A:G.157, A:T.158, A:T.158, A:G.191, A:G.435, A:E.436, B:Q.340, B:R.343, B:A.408, B:G.411 Salt bridges: B:R.320, B:R.320 pi-Stacking: B:Y.337 FAD.4: 25 residues within 4Å: Chain A: R.320, Q.322, V.334, Y.337, T.339, Q.340, R.343, A.408, G.410, G.411, Y.414 Chain B: L.115, Y.149, Q.151, T.152, G.157, T.158, W.189, P.190, G.191, T.432, Y.433, E.436, M.438, V.439 25 PLIP interactions: 14 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:Y.433, B:Y.433, A:Y.414, A:Y.414 Hydrogen bonds: B:Y.149, B:Q.151, B:T.152, B:T.152, B:G.157, B:T.158, B:T.158, B:G.191, B:N.250, B:E.436, A:T.339, A:R.343, A:G.411 Water bridges: B:E.436, A:Q.322, A:Y.337, A:Y.337 pi-Stacking: B:W.189, A:Y.337 Salt bridges: A:R.320, A:R.320

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.577 Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: D.577 Ligands: ATP.3 No protein-ligand interaction detected (PLIP)

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 13 residues within 4Å: Chain A: S.392, H.396, N.437, M.438, L.441, R.533, R.536, Y.581 Chain B: H.342, R.343, Q.404, Y.573 Ligands: MG.6 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.392, A:R.536, B:R.343, B:Q.404 Salt bridges: A:R.533, A:R.533, A:R.536, A:R.536, A:R.536, B:H.342 pi-Stacking: A:H.396, A:H.396 ATP.5: 14 residues within 4Å: Chain A: H.342, R.343, F.347, Q.404, Y.573 Chain B: S.392, H.396, N.437, M.438, L.441, R.533, R.536, Y.581 Ligands: MG.2 15 PLIP interactions: 5 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:R.343, A:Q.404, A:Y.573, A:Y.573, B:S.392, B:R.536 Salt bridges: A:H.342, B:R.533, B:R.533, B:R.536, B:R.536, B:R.536 Water bridges: B:N.437 pi-Stacking: B:H.396, B:H.396

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Structural characterization of acyl-CoA oxidases reveals a direct link between pheromone biosynthesis and metabolic state in Caenorhabditis elegans. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-08-24

Peptides

Acyl-coenzyme A oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

Acyl-coenzyme A oxidase

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