Research workbench
Crystal structure of tomato beta-galactosidase 4
Analyse Crystal structure of tomato beta-galactosidase 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W5F
- Type
- protein
- Length
- 1,402 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
- ARG, NAG, CL
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-galactosidase (EC 3.2.1.23) | protein | 701 | 21% helix, 33% strand | O81100 |
Ligands and binding sites
- ARG · Arginine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- CL · Chloride ion · ion · 9 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.76 | 0.79 | 96 | EPE |
| 2 | 271 | 0.61 | 0.79 | 37 | empty |
| 3 | 206 | 0.54 | 0.78 | 39 | EPE |
| 4 | 257 | 0.51 | 0.75 | 34 | empty |
| 5 | 118 | 0.48 | 0.79 | 23 | EPE |
Interfaces
1 interface between chains.
- A–B · 510 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3W5F · Crystal structure of tomato beta-galactosidase 4 · 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 3W5F · PDBe 3W5F · UniProt O81100
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