Research workbench
The crystal structure of mandelate oxidase Y128C with benzoyl-formic acid
Analyse The crystal structure of mandelate oxidase Y128C with benzoyl-formic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZZZ
- Type
- protein
- Length
- 332 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxymandelate oxidase
- EC
- 1.1.3.46
- UniProt
- O52792
- Ligands
- FMN, 173
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxymandelate oxidase (EC 1.1.3.46) | protein | 332 | 45% helix, 14% strand | O52792 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.76 | 0.88 | 46 | FMN, 173 |
| 2 | 111 | 0.41 | 0.76 | 24 | empty |
| 3 | 85 | 0.33 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5ZZZ · The crystal structure of Mandelate oxidase Y128C with benzoyl-formic acid · the same entry in another collection · chain A against A, TM-score 1.00
- O52792 · AlphaFold monomer V2.0 prediction for 4-hydroxymandelate oxidase (O52792) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 O52792
- Elsewhere: RCSB PDB 5ZZZ · PDBe 5ZZZ · UniProt O52792
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