MolNFT v1 · #135743 · protein
Acid ceramidase (ASAH1, acdase) from common minke whale, CYS143ALA, uncleaved
5U84: “Acid ceramidase (ASAH1, acdase) from common minke whale, CYS143ALA, uncleaved”. X-ray diffraction, 4 ligands (I3C, NAG, FUC), 7 pockets (best druggability 0.73). MolNFT v1 #135743 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5U84
- Type
- protein
- Length
- 705 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acid ceramidase
- EC
- 3.5.1.23
- UniProt
- A0A383ZFX3
- Ligands
- I3C, NAG, FUC, IOD
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acid ceramidase (EC 3.5.1.23) | protein | 352 | 36% helix, 28% strand | A0A383ZFX3 |
| B | Acid ceramidase (EC 3.5.1.23) | protein | 353 | 35% helix, 27% strand | A0A383ZFX3 |
Ligands and binding sites
- I3C · 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid · ligand · 9 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- IOD · Iodide ion · ion · 34 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.73 | 0.85 | 30 | I3C |
| 2 | 193 | 0.73 | 0.88 | 29 | IOD |
| 3 | 288 | 0.55 | 0.75 | 39 | IOD |
| 4 | 240 | 0.53 | 0.76 | 37 | IOD |
| 5 | 83 | 0.42 | 0.79 | 21 | IOD |
Interfaces
1 interface between chains.
- A–B · 1067 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5U84 · Acid ceramidase (ASAH1, aCDase) from common minke whale, 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 A0A383ZFX3
- Elsewhere: RCSB PDB 5U84 · PDBe 5U84 · UniProt A0A383ZFX3
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