Research workbench
Sweet potato purple acid PHOSPHATASE/PHOSPHATE complex
Analyse Sweet potato purple acid PHOSPHATASE/PHOSPHATE complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XZW
- Type
- protein
- Length
- 850 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purple acid phosphatase
- EC
- 3.1.3.2
- Ligands
- NAG, FUC, MAN, FE, MN, PO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purple acid phosphatase (EC 3.1.3.2) | protein | 424 | 19% helix, 30% strand | — |
| B | Purple acid phosphatase (EC 3.1.3.2) | protein | 426 | 19% helix, 30% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.69 | 0.81 | 39 | empty |
| 2 | 366 | 0.67 | 0.80 | 37 | empty |
| 3 | 92 | 0.39 | 0.76 | 24 | empty |
| 4 | 63 | 0.34 | 0.77 | 15 | PO4 |
| 5 | 71 | 0.34 | 0.76 | 20 | PO4 |
Interfaces
1 interface between chains.
- A–B · 1649 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 1XZW · Sweet potato purple acid phosphatase/phosphate complex · the same entry in another collection · 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
- Elsewhere: RCSB PDB 1XZW · PDBe 1XZW
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