Research workbench
Structure of E298Q-beta-galactosidase from aspergillus niger in complex with 6-galactosyl-lactose
Analyse Structure of E298Q-beta-galactosidase from aspergillus niger in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MGD
- 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
- MAN, NAG, BMA, GAL, GLC, CL
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable beta-galactosidase a (EC 3.2.1.23) | protein | 968 | 16% helix, 35% strand | A2QAN3 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 15 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- CL · Chloride ion · ion · chains A
- DMS · Dimethyl sulfoxide · 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
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 | 200 | 0.61 | 0.82 | 33 | empty |
| 2 | 157 | 0.44 | 0.75 | 30 | GAL, 1PE |
| 3 | 143 | 0.42 | 0.75 | 19 | NAG |
| 4 | 69 | 0.39 | 0.79 | 24 | empty |
| 5 | 82 | 0.34 | 0.75 | 20 | empty |
Modifications
Observed in the structure: 9 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5MGD · 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 5MGD · PDBe 5MGD · UniProt A2QAN3
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