Research workbench
Truncated beta-galactosidase III from Bifidobacterium bifidum
Analyse Truncated beta-galactosidase III from Bifidobacterium bifidum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QUC
- Type
- protein
- Length
- 1,718 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Bifidobacterium bifidum
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- Q9F4D5
- Ligands
- CA
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.3 · 1 distinct chain · 14% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-galactosidase (EC 3.2.1.23) | protein | 859 | 14% helix, 38% strand | Q9F4D5 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
- IMD · Imidazole · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.75 | 0.78 | 109 | empty |
| 2 | 1194 | 0.75 | 0.78 | 100 | empty |
| 3 | 63 | 0.74 | 0.99 | 21 | IMD |
| 4 | 53 | 0.73 | 0.99 | 20 | IMD |
| 5 | 469 | 0.69 | 0.80 | 44 | empty |
Interfaces
1 interface between chains.
- A–B · 333 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6QUC · Truncated beta-galactosidase III from bifidobacterium bifidum · 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 Q9F4D5
- Elsewhere: RCSB PDB 6QUC · PDBe 6QUC · UniProt Q9F4D5
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