MolNFT v1 · #58861 · protein
Crystal structure of beta-galactosidase from bacteroides thetaiotaomicron vpi-5482
3BGA: “Crystal structure of beta-galactosidase from bacteroides thetaiotaomicron vpi-5482”. X-ray diffraction, 3 ligands (NA, MG, CL), 20 pockets (best druggability 0.76). MolNFT v1 #58861 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3BGA
- Type
- protein
- Length
- 2,003 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- UniProt
- Q8A799
- Ligands
- NA, MG, CL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactosidase | protein | 1003 | 15% helix, 39% strand | Q8A799 |
| B | Beta-galactosidase | protein | 1000 | 15% helix, 38% strand | Q8A799 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.76 | 0.97 | 25 | empty |
| 2 | 61 | 0.71 | 0.97 | 23 | empty |
| 3 | 529 | 0.69 | 0.79 | 41 | empty |
| 4 | 468 | 0.69 | 0.80 | 44 | empty |
| 5 | 169 | 0.67 | 0.87 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 932 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 3BGA · Crystal structure of beta-galactosidase from Bacteroides thetaiotaomicron VPI-5482 · 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 Q8A799
- Elsewhere: RCSB PDB 3BGA · PDBe 3BGA · UniProt Q8A799
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