SMTL ID : 7q84.1

Crystal structure of human peroxisomal acyl-Co-A oxidase 1a, apo-form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 12 residues within 4Å: Chain A: R.314, Q.316, I.328, G.404, G.405 Chain B: G.151, T.152, T.426, F.427 Ligands: EDO.2, EDO.3, PEG.4 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.151, B:T.152, A:R.314, A:R.314, A:G.405 PGE.10: 10 residues within 4Å: Chain A: T.146, G.151, T.152, T.426, F.427 Chain B: R.314, Q.316, G.404, G.405 Ligands: EDO.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.314 Water bridges: B:Y.310, B:G.405

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 9 residues within 4Å: Chain A: R.314, G.405, H.406 Chain B: E.147, M.148, H.150, G.151, W.183 Ligands: PGE.1 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:H.150, B:H.150, A:R.314, A:R.314, A:G.405, A:H.406 EDO.3: 8 residues within 4Å: Chain A: Q.334, K.337, M.401, A.402, G.404 Chain B: E.430 Ligands: PGE.1, PEG.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.334, A:K.337 Water bridges: A:K.337 EDO.5: 3 residues within 4Å: Chain A: Q.620, D.621, Y.631 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.621, A:D.621 Water bridges: A:V.622, A:Y.631 EDO.6: 4 residues within 4Å: Chain A: L.30, D.31, R.40, F.617 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.40, A:Q.349 EDO.8: 4 residues within 4Å: Chain A: F.387, W.390, M.435, E.535 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.535 EDO.9: 4 residues within 4Å: Chain A: T.152, V.433 Chain B: S.317, F.331 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.317, B:S.317 Water bridges: B:T.333, B:T.333 EDO.11: 7 residues within 4Å: Chain A: E.430 Chain B: Q.334, K.337, M.401, A.402, G.404 Ligands: PGE.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.334, B:K.337 EDO.12: 6 residues within 4Å: Chain B: F.53, K.73, F.98, V.99, R.101, V.622 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.73, B:V.99, B:R.101 EDO.13: 4 residues within 4Å: Chain B: F.619, Q.620, D.621, Y.631 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.621 Water bridges: B:F.619, B:F.619, B:V.622, B:Y.631, B:Y.631 EDO.15: 4 residues within 4Å: Chain B: L.30, D.31, Q.349, F.617 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.349, B:F.617 Water bridges: B:Q.349

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 10 residues within 4Å: Chain A: Q.316, S.317, I.328, F.331, T.333 Chain B: T.152, V.433, L.436 Ligands: PGE.1, EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.333 Water bridges: A:T.333

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: V.528, D.529, R.532 Chain B: Y.336, S.575, Q.576, N.596 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.529, A:R.532, B:Y.336, B:S.575, B:Q.576 GOL.14: 3 residues within 4Å: Chain B: S.18, A.19, S.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.19 Water bridges: B:S.20 GOL.16: 6 residues within 4Å: Chain B: M.81, R.82, I.86, A.87, I.92, L.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sonani, R.R. et al., Crystal structures of apo- and FAD-bound human peroxisomal acyl-CoA oxidase provide mechanistic basis explaining clinical observations. Int.J.Biol.Macromol. (2022)

Release Date

2022-03-02

Peptides

Isoform 2 of Peroxisomal acyl-coenzyme A oxidase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoform 2 of Peroxisomal acyl-coenzyme A oxidase 1

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