MolNFT v1 · #140968 · protein
Crystal structure of acyl-CoA OXIDASE3 from yarrowia lipolytica
5YS9 · Acyl-coenzyme a oxidase 3: “Crystal structure of acyl-CoA OXIDASE3 from yarrowia lipolytica”. X-ray diffraction, 1 ligand (FAD), 15 pockets (best druggability 0.85). MolNFT v1 #140968 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YS9
- Type
- protein
- Length
- 1,383 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-coenzyme a oxidase 3
- EC
- 1.3.3.6
- UniProt
- O74936
- Ligands
- FAD
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-coenzyme a oxidase 3 (EC 1.3.3.6) | protein | 692 | 58% helix, 10% strand | O74936 |
| B | Acyl-coenzyme a oxidase 3 (EC 1.3.3.6) | protein | 691 | 60% helix, 10% strand | O74936 |
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
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.85 | 0.85 | 98 | FAD |
| 2 | 1140 | 0.84 | 0.85 | 120 | FAD |
| 3 | 747 | 0.84 | 0.87 | 83 | empty |
| 4 | 663 | 0.82 | 0.87 | 108 | empty |
| 5 | 195 | 0.77 | 0.92 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 5867 Ų buried · 76 hydrogen bonds · protein-protein
Compared structures
- 5YS9 · Crystal structure of acyl-coA oxidase3 from Yarrowia lipolytica · the same entry in another collection · chain A against A, TM-score 1.00
- O74936 · AlphaFold monomer V2.0 prediction for acyl-coenzyme a oxidase 3 (O74936) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O74936
- Elsewhere: RCSB PDB 5YS9 · PDBe 5YS9 · UniProt O74936
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