Research workbench
Crystal structure of L-phenylalanine oxidase from psuedomonas SP.P501
Analyse Crystal structure of L-phenylalanine oxidase from psuedomonas SP.P501 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YR5
- 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, SO4
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 23% 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, 23% strand | Q5W9R9 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.86 | 0.88 | 108 | SO4, FAD, GOL |
| 2 | 1100 | 0.86 | 0.87 | 147 | SO4, FAD, GOL |
| 3 | 669 | 0.71 | 0.78 | 84 | empty |
| 4 | 193 | 0.68 | 0.86 | 34 | empty |
| 5 | 206 | 0.65 | 0.83 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 3699 Ų buried · 58 hydrogen bonds · protein-protein
Compared structures
- 2YR5 · Crystal structure of L-phenylalanine oxidase from Psuedomonas sp.P501 · 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 2YR5 · PDBe 2YR5 · UniProt Q5W9R9
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