Research workbench
Crystal structure of bifidobacterium bifidum beta-galactosidase in complex with alpha-galactose
Analyse Crystal structure of bifidobacterium bifidum beta-galactosidase 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
- 4UCF
- Type
- protein
- Length
- 2,052 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- E3EPA1
- Ligands
- GLA
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactosidase (EC 3.2.1.23) | protein | 682 | 33% helix, 24% strand | E3EPA1 |
| B | Beta-galactosidase (EC 3.2.1.23) | protein | 686 | 33% helix, 23% strand | E3EPA1 |
| C | Beta-galactosidase (EC 3.2.1.23) | protein | 684 | 33% helix, 23% strand | E3EPA1 |
Ligands and binding sites
- GLA · alpha-D-galactopyranose · sugar · 7 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains C
- POL · N-propanol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.73 | 0.99 | 19 | empty |
| 2 | 55 | 0.72 | 0.98 | 19 | empty |
| 3 | 770 | 0.69 | 0.76 | 78 | GLA |
| 4 | 746 | 0.68 | 0.75 | 87 | GLA |
| 5 | 58 | 0.68 | 0.96 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2696 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 2645 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2640 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 glycan (glycosylation).
Compared structures
- 4UCF · Crystal structure of Bifidobacterium bifidum beta-galactosidase in complex with… · 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 E3EPA1
- Elsewhere: RCSB PDB 4UCF · PDBe 4UCF · UniProt E3EPA1
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