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Crystal structure of tomato beta-galactosidase (tbg) 4 with beta-1,4- galactobiose
Analyse Crystal structure of tomato beta-galactosidase (tbg) 4 with beta-1,4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IK6
- 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
- NAG, GAL, CL
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-galactosidase (EC 3.2.1.23) | protein | 705 | 21% helix, 32% strand | O81100 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 4 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
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 | 884 | 0.78 | 0.81 | 104 | GAL |
| 2 | 311 | 0.62 | 0.79 | 40 | empty |
| 3 | 316 | 0.62 | 0.79 | 43 | empty |
| 4 | 500 | 0.59 | 0.74 | 45 | empty |
| 5 | 249 | 0.58 | 0.78 | 38 | GAL |
Interfaces
1 interface between chains.
- A–B · 756 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation, glycation).
Compared structures
- 6IK6 · Crystal structure of Tomato beta-galactosidase (TBG) 4 with beta-1,4-galactobiose · 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 6IK6 · PDBe 6IK6 · UniProt O81100
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