MolNFT v1 · #122119 · protein
Structure of beta-galactosidase from aspergillus niger
5IFP · Beta-galactosidase a: “Structure of beta-galactosidase from aspergillus niger”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 6 pockets (best druggability 0.61). MolNFT v1 #122119 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5IFP
- Type
- protein
- Length
- 968 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase a
- EC
- 3.2.1.23
- UniProt
- A2QAN3
- Ligands
- NAG, MAN, BMA, SO4, CL
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactosidase a (EC 3.2.1.23) | protein | 968 | 16% helix, 34% strand | A2QAN3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 13 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 5 copies · chains A
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
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 | 228 | 0.61 | 0.81 | 39 | empty |
| 2 | 164 | 0.47 | 0.76 | 32 | BTB, GOL |
| 3 | 53 | 0.47 | 0.85 | 23 | empty |
| 4 | 112 | 0.39 | 0.75 | 17 | NAG, GOL |
| 5 | 77 | 0.35 | 0.76 | 22 | empty |
Modifications
Observed in the structure: 10 glycan, 2 disulfide (N-glycosylation, disulfide).
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 A2QAN3
- Elsewhere: RCSB PDB 5IFP · PDBe 5IFP · UniProt A2QAN3
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