Research workbench
X-ray crystal structure of LEACX1, an acyl-CoA oxidase from lycopersicon esculentum (tomato)
Analyse X-ray crystal structure of LEACX1, an acyl-CoA oxidase from lycopersicon… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FON
- Type
- protein
- Length
- 1,963 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisomal acyl-CoA oxidase 1A
- EC
- 1.3.3.6
- UniProt
- Q5D8D3
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisomal acyl-CoA oxidase 1A (EC 1.3.3.6) | protein | 654 | 60% helix, 11% strand | Q5D8D3 |
| B | Peroxisomal acyl-CoA oxidase 1A (EC 1.3.3.6) | protein | 656 | 61% helix, 11% strand | Q5D8D3 |
| C | Peroxisomal acyl-CoA oxidase 1A (EC 1.3.3.6) | protein | 653 | 55% helix, 9% strand | Q5D8D3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.88 | 0.89 | 104 | FAD |
| 2 | 1055 | 0.88 | 0.89 | 109 | FAD |
| 3 | 990 | 0.85 | 0.85 | 104 | FAD |
| 4 | 265 | 0.76 | 0.88 | 41 | empty |
| 5 | 209 | 0.73 | 0.89 | 44 | empty |
Interfaces
2 interfaces between chains.
- A–B · 5384 Ų buried · 67 hydrogen bonds · protein-protein
- A–C · 100 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2FON · X-ray crystal structure of LeACX1, an acyl-CoA oxidase from Lycopersicon esculentum… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q5D8D3
- Elsewhere: RCSB PDB 2FON · PDBe 2FON · UniProt Q5D8D3
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