Research workbench
X-ray crystal structures of L-phenylalanine oxidase (deaminating and decaboxylating) from pseudomonas sp. P501. structures of the enzyme- ligand complex and catalytic mechanism
Analyse X-ray crystal structures of L-phenylalanine oxidase (deaminating and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AYJ
- 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, PHE, SO4
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 36% 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 | 36% helix, 22% strand | Q5W9R9 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- PHE · Phenylalanine · 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
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.87 | 0.89 | 113 | FAD, PHE, GOL |
| 2 | 865 | 0.86 | 0.88 | 102 | FAD, PHE, GOL |
| 3 | 716 | 0.71 | 0.78 | 93 | empty |
| 4 | 215 | 0.66 | 0.84 | 34 | empty |
| 5 | 227 | 0.65 | 0.83 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 3721 Ų buried · 59 hydrogen bonds · protein-protein
Compared structures
- 3AYJ · 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 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 Q5W9R9
- Elsewhere: RCSB PDB 3AYJ · PDBe 3AYJ · UniProt Q5W9R9
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