MolNFT v1 · #70866 · protein
Interconversion of human lysosomal enzyme specificities
3LXB · Alpha-galactosidase a: “Interconversion of human lysosomal enzyme specificities”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 6 pockets (best druggability 0.54). MolNFT v1 #70866 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3LXB
- Type
- protein
- Length
- 791 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-galactosidase a
- EC
- 3.2.1.22
- UniProt
- P06280
- Ligands
- NAG, BMA, MAN
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-galactosidase a (EC 3.2.1.22) | protein | 395 | 32% helix, 24% strand | P06280 |
| B | Alpha-galactosidase a (EC 3.2.1.22) | protein | 396 | 33% helix, 24% strand | P06280 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 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
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.54 | 0.74 | 36 | empty |
| 2 | 117 | 0.42 | 0.77 | 20 | empty |
| 3 | 63 | 0.42 | 0.81 | 23 | empty |
| 4 | 131 | 0.41 | 0.75 | 22 | empty |
| 5 | 51 | 0.35 | 0.79 | 15 | GOL |
Interfaces
1 interface between chains.
- A–B · 1110 Ų buried · 18 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 P06280
- Elsewhere: RCSB PDB 3LXB · PDBe 3LXB · UniProt P06280
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