Research workbench
Acid ceramidase (ASAH1, acdase) from naked mole rat, CYS143ALA, uncleaved
Analyse Acid ceramidase (ASAH1, acdase) from naked mole rat, CYS143ALA, uncleaved in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U81
- Type
- protein
- Length
- 369 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acid ceramidase isoform B
- EC
- 3.5.1.23
- UniProt
- A0A0P6JG37
- Ligands
- NAG, MAN, BMA, FUC, CL
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acid ceramidase isoform B (EC 3.5.1.23) | protein | 369 | 34% helix, 28% strand | A0A0P6JG37 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.47 | 0.75 | 20 | empty |
| 2 | 128 | 0.46 | 0.77 | 22 | empty |
| 3 | 54 | 0.32 | 0.77 | 14 | empty |
Modifications
Observed in the structure: 3 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5U81 · Acid ceramidase (ASAH1, aCDase) from naked mole rat, Cys143Ala, uncleaved · 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 A0A0P6JG37
- Elsewhere: RCSB PDB 5U81 · PDBe 5U81 · UniProt A0A0P6JG37
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