MolNFT v1 · #161958 · protein
Truncated beta-galactosidase III from bifidobacterium bifidum in complex with galactose
6QUB: “Truncated beta-galactosidase III from bifidobacterium bifidum in complex with galactose”. X-ray diffraction, 2 ligands (GAL, CA), 18 pockets (best druggability 0.76). MolNFT v1 #161958 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6QUB
- Type
- protein
- Length
- 1,714 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- Q9F4D5
- Ligands
- GAL, CA
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 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 | 857 | 14% helix, 38% strand | Q9F4D5 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.76 | 0.99 | 23 | empty |
| 2 | 1191 | 0.75 | 0.78 | 106 | empty |
| 3 | 696 | 0.74 | 0.81 | 71 | empty |
| 4 | 57 | 0.73 | 0.99 | 22 | empty |
| 5 | 698 | 0.66 | 0.75 | 80 | empty |
Interfaces
1 interface between chains.
- A–B · 274 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6QUB · Truncated beta-galactosidase III from Bifidobacterium bifidum in complex with galactose · 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 6QUB · PDBe 6QUB · UniProt Q9F4D5
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