Research workbench
Crystal structure of tomato beta-galactosidase 4 in complex with galactose
Analyse Crystal structure of tomato beta-galactosidase 4 in complex with galactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W5G
- Type
- protein
- Length
- 1,410 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- O81100
- Ligands
- GAL, NAG
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-galactosidase (EC 3.2.1.23) | protein | 705 | 20% helix, 32% strand | O81100 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 8 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.67 | 0.78 | 75 | GAL |
| 2 | 318 | 0.64 | 0.80 | 38 | empty |
| 3 | 286 | 0.62 | 0.80 | 38 | empty |
| 4 | 201 | 0.55 | 0.78 | 38 | GAL |
| 5 | 259 | 0.52 | 0.75 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 341 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3W5G · Crystal structure of tomato beta-galactosidase 4 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 O81100
- Elsewhere: RCSB PDB 3W5G · PDBe 3W5G · UniProt O81100
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