MolNFT v1 · #58275 · protein
X-ray crystal structures of L-phenylalanine oxidase (deaminating and decaboxylating) from pseudomonas sp. P501. structures of the enzyme- ligand complex and catalytic mechanism
3AYI · Pro-enzyme of L-phenylalanine oxidase: “X-ray crystal structures of L-phenylalanine oxidase (deaminating and decaboxylating) from pseudomonas sp.…”. X-ray diffraction, 3 ligands (FAD, HCI, SO4), 11 pockets (best druggability 0.86).…
- PDB
- 3AYI
- Type
- protein
- Length
- 1,368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pro-enzyme of L-phenylalanine oxidase
- EC
- 1.13.12.9
- UniProt
- Q5W9R9
- Ligands
- FAD, HCI, SO4
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pro-enzyme of L-phenylalanine oxidase (EC 1.13.12.9) | protein | 684 | 35% helix, 22% strand | Q5W9R9 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- HCI · Hydrocinnamic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.86 | 0.87 | 147 | FAD, HCI, GOL |
| 2 | 867 | 0.86 | 0.88 | 104 | FAD, HCI, GOL |
| 3 | 624 | 0.71 | 0.79 | 83 | empty |
| 4 | 188 | 0.67 | 0.86 | 34 | empty |
| 5 | 211 | 0.65 | 0.84 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 3704 Ų buried · 60 hydrogen bonds · protein-protein
Compared structures
- 3AYI · X-ray crystal structures of L-phenylalanine oxidase (deaminating and decaboxylating) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5W9R9 · AlphaFold monomer V2.0 prediction for phenylalanine 2-monooxygenase precursor (Q5W9R9) · a predicted model of the same protein · chain A 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 Q5W9R9
- Elsewhere: RCSB PDB 3AYI · PDBe 3AYI · UniProt Q5W9R9
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