Research workbench
Crystal structure of acyl-CoA OXIDASE1 from yarrowia lipolytica
Analyse Crystal structure of acyl-CoA OXIDASE1 from yarrowia lipolytica in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y9D
- Type
- protein
- Length
- 1,369 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-coenzyme a oxidase 1
- EC
- 1.3.3.6
- UniProt
- O74934
- Ligands
- FAD
- Pockets
- 17 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-coenzyme a oxidase 1 (EC 1.3.3.6) | protein | 687 | 59% helix, 9% strand | O74934 |
| B | Acyl-coenzyme a oxidase 1 (EC 1.3.3.6) | protein | 682 | 59% helix, 10% strand | O74934 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.88 | 0.90 | 122 | FAD |
| 2 | 1030 | 0.85 | 0.86 | 109 | FAD |
| 3 | 914 | 0.85 | 0.86 | 92 | empty |
| 4 | 479 | 0.85 | 0.92 | 58 | empty |
| 5 | 160 | 0.61 | 0.84 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 5607 Ų buried · 66 hydrogen bonds · protein-protein
Compared structures
- 5Y9D · Crystal structure of acyl-coA oxidase1 from Yarrowia lipolytica · the same entry in another collection · chain A against A, TM-score 1.00
- O74934 · AlphaFold monomer V2.0 prediction for acyl-coenzyme a oxidase 1 (O74934) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O74934
- Elsewhere: RCSB PDB 5Y9D · PDBe 5Y9D · UniProt O74934
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.