Research workbench
Beta-(1,6)-galactosidase from bifidobacterium animalis subsp. lactis bl-04 nucleophile mutant E324A in complex with galactose
Analyse Beta-(1,6)-galactosidase from bifidobacterium animalis subsp. lactis bl-04… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UOZ
- Type
- protein
- Length
- 2,064 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- C6A6W5
- Ligands
- GLA, ZN
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Beta-galactosidase (EC 3.2.1.23) | protein | 688 | 34% helix, 23% strand | C6A6W5 |
Ligands and binding sites
- GLA · alpha-D-galactopyranose · sugar · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · chains A, B, C
- PGE · Triethylene glycol · additive · 6 copies · chains A, B, 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 | 884 | 0.73 | 0.77 | 76 | GLA, PGE |
| 2 | 872 | 0.73 | 0.77 | 81 | GLA, PGE |
| 3 | 58 | 0.72 | 0.99 | 22 | empty |
| 4 | 887 | 0.72 | 0.77 | 78 | GLA, PGE |
| 5 | 138 | 0.72 | 0.91 | 34 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2772 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2763 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2759 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 4UOZ · beta-(1,6)-galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 nucleophile… · 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 C6A6W5
- Elsewhere: RCSB PDB 4UOZ · PDBe 4UOZ · UniProt C6A6W5
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