Research workbench
Human acid ceramidase (ASAH1, acdase) self-activated
Analyse Human acid ceramidase (ASAH1, acdase) self-activated in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U7Z
- Type
- protein
- Length
- 732 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acid ceramidase
- UniProt
- A8K0B6
- Ligands
- NAG, BMA, SO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Acid ceramidase | protein | 113 | 60% helix, 8% strand | A8K0B6 |
| B, D | Acid ceramidase | protein | 253 | 23% helix, 34% strand | A8K0B6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.79 | 0.85 | 60 | SO4 |
| 2 | 346 | 0.75 | 0.85 | 43 | empty |
| 3 | 436 | 0.60 | 0.75 | 40 | empty |
| 4 | 190 | 0.57 | 0.80 | 22 | SO4 |
| 5 | 166 | 0.41 | 0.73 | 25 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3007 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2985 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 243 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 5U7Z · Human acid ceramidase (ASAH1, aCDase) self-activated · 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
- Every structure of UniProt A8K0B6
- Elsewhere: RCSB PDB 5U7Z · PDBe 5U7Z · UniProt A8K0B6
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