MolNFT v1 · #73740 · protein
Structure of the beta-galactosidase from kluyveromyces lactis in complex with galactose
3OB8: “Structure of the beta-galactosidase from kluyveromyces lactis in complex with galactose”. X-ray diffraction, 4 ligands (GAL, NA, MG), 20 pockets (best druggability 0.85). MolNFT v1 #73740 on GenesisL1: 3D structure, binding sites…
- PDB
- 3OB8
- Type
- protein
- Length
- 4,096 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- P00723
- Ligands
- GAL, NA, MG, MN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, C | Beta-galactosidase (EC 3.2.1.23) | protein | 1024 | 16% helix, 39% strand | P00723 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, D, C
- NA · Sodium ion · metal · 16 copies · chains A, B, D, C
- MG · Magnesium ion · metal · 4 copies · chains A, B, D, C
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, D, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.85 | 0.88 | 84 | empty |
| 2 | 1030 | 0.85 | 0.86 | 101 | empty |
| 3 | 887 | 0.79 | 0.82 | 85 | empty |
| 4 | 586 | 0.78 | 0.84 | 69 | empty |
| 5 | 215 | 0.78 | 0.92 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–C · 2623 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 2622 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2558 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 401 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 369 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3OB8 · Structure of the beta-galactosidase from Kluyveromyces lactis in complex with galactose · the same entry in another collection · chain C against C, TM-score 1.00
- P00723 · AlphaFold monomer V2.0 prediction for beta-galactosidase (P00723) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P00723
- Elsewhere: RCSB PDB 3OB8 · PDBe 3OB8 · UniProt P00723
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