Research workbench
X-ray structures and mechanistic implications of three functional derivatives of ascorbate oxidase from zucchini: reduced-, peroxide-, and azide-forms
Analyse X-ray structures and mechanistic implications of three functional derivatives… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ASP
- Type
- protein
- Length
- 1,104 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ascorbate oxidase
- EC
- 1.10.3.3
- UniProt
- P37064
- Ligands
- PEO, NAG, CU, OH
- Pockets
- 14 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ascorbate oxidase (EC 1.10.3.3) | protein | 552 | 10% helix, 38% strand | P37064 |
Ligands and binding sites
- PEO · Hydrogen peroxide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CU · Copper (II) ion · metal · 9 copies · chains A, B
- OH · Hydroxide ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.70 | 0.78 | 51 | empty |
| 2 | 638 | 0.69 | 0.77 | 54 | empty |
| 3 | 189 | 0.57 | 0.80 | 27 | empty |
| 4 | 198 | 0.56 | 0.79 | 29 | empty |
| 5 | 118 | 0.51 | 0.81 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 768 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1ASP · X-ray structures and mechanistic implications of three functional derivatives of… · the same entry in another collection · chain A against A, TM-score 1.00
- P37064 · AlphaFold monomer V2.0 prediction for L-ascorbate oxidase (P37064) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P37064
- Elsewhere: RCSB PDB 1ASP · PDBe 1ASP · UniProt P37064
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