Research workbench
PH 2.5 acid phosphatase from aspergillus niger
Analyse PH 2.5 acid phosphatase from aspergillus niger in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QFX
- Type
- protein
- Length
- 884 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (pH 2.5 acid phosphatase)
- EC
- 3.1.3.8
- UniProt
- P34755
- Ligands
- NAG, MAN, BMA, SO4
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (pH 2.5 acid phosphatase) (EC 3.1.3.8) | protein | 441 | 40% helix, 13% strand | P34755 |
| B | Protein (pH 2.5 acid phosphatase) (EC 3.1.3.8) | protein | 443 | 41% helix, 13% strand | P34755 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
- SO4 · Sulfate ion · ion · 11 copies · chains A, B
- GOL · Glycerol · additive · 6 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.82 | 0.83 | 76 | SO4 |
| 2 | 348 | 0.56 | 0.75 | 41 | SO4, GOL |
| 3 | 320 | 0.54 | 0.75 | 33 | SO4, GOL |
| 4 | 137 | 0.48 | 0.79 | 19 | empty |
| 5 | 132 | 0.47 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2760 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
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 P34755
- Elsewhere: RCSB PDB 1QFX · PDBe 1QFX · UniProt P34755
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