MolNFT v1 · #122122 · protein
Structure of E298Q-beta-galactosidase from aspergillus niger in complex with 3-B-galactopyranosyl glucose
5IFT · Probable beta-galactosidase a: “Structure of E298Q-beta-galactosidase from aspergillus niger in complex with 3-B-galactopyranosyl glucose”. X-ray diffraction, 7 ligands (NAG, MAN, BMA), 5 pockets (best druggability 0.60). MolNFT v1…
- PDB
- 5IFT
- Type
- protein
- Length
- 968 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable beta-galactosidase a
- EC
- 3.2.1.23
- UniProt
- A2QAN3
- Ligands
- NAG, MAN, BMA, GLC, GAL, SO4, CL
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable 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 · 12 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · chains A
- CL · Chloride ion · ion · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.60 | 0.82 | 35 | empty |
| 2 | 142 | 0.46 | 0.77 | 27 | GLC, GAL |
| 3 | 110 | 0.38 | 0.75 | 18 | NAG |
| 4 | 53 | 0.37 | 0.80 | 14 | empty |
| 5 | 72 | 0.33 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 9 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5IFT · STRUCTURE OF E298Q-BETA-GALACTOSIDASE FROM ASPERGILLUS NIGER IN COMPLEX WITH… · the same entry in another collection · chain A against A, TM-score 1.00
- A2QAN3 · AlphaFold monomer V2.0 prediction for beta-galactosidase a (A2QAN3) · a predicted model of the same protein · 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 A2QAN3
- Elsewhere: RCSB PDB 5IFT · PDBe 5IFT · UniProt A2QAN3
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