Research workbench
Crystal structure of the human N-acetyl-alpha-glucosaminidase
Analyse Crystal structure of the human N-acetyl-alpha-glucosaminidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XWH
- Type
- protein
- Length
- 720 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-N-acetylglucosaminidase
- EC
- 3.2.1.50
- UniProt
- P54802
- Ligands
- XYL, NAG, BMA
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-N-acetylglucosaminidase (EC 3.2.1.50) | protein | 720 | 51% helix, 11% strand | P54802 |
Ligands and binding sites
- XYL · Xylitol · ligand · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.75 | 0.91 | 43 | empty |
| 2 | 275 | 0.71 | 0.86 | 25 | empty |
| 3 | 51 | 0.70 | 0.98 | 16 | empty |
| 4 | 179 | 0.68 | 0.87 | 34 | XYL |
| 5 | 186 | 0.59 | 0.82 | 37 | empty |
Modifications
Observed in the structure: 6 glycan, 2 disulfide, 1 modified (N-glycosylation, disulfide, phosphorylation).
Compared structures
- 4XWH · Crystal structure of the human N-acetyl-alpha-glucosaminidase · the same entry in another collection · chain A against A, TM-score 1.00
- P54802 · AlphaFold monomer V2.0 prediction for alpha-N-acetylglucosaminidase (P54802) · 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 P54802
- Elsewhere: RCSB PDB 4XWH · PDBe 4XWH · UniProt P54802
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