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
- 1ASQ
- 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
- NAG, CU, AZI, OH
- Pockets
- 15 · best druggability 0.71
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
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CU · Copper (II) ion · metal · 9 copies · chains A, B
- AZI · Azide ion · ion · 4 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
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.71 | 0.76 | 56 | empty |
| 2 | 906 | 0.70 | 0.75 | 64 | empty |
| 3 | 191 | 0.57 | 0.80 | 32 | AZI |
| 4 | 189 | 0.55 | 0.80 | 31 | AZI |
| 5 | 116 | 0.48 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 756 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1ASQ · 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 1ASQ · PDBe 1ASQ · UniProt P37064
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.