Research workbench
Crystal structure of native 6-phospho-glucosidase lpbgl from lactobacillus plantarum
Analyse Crystal structure of native 6-phospho-glucosidase lpbgl from lactobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NAQ
- Type
- protein
- Length
- 2,766 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.21
- UniProt
- F9ULH8
- Ligands
- PO4
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Beta-galactosidase (EC 3.2.1.21) | protein | 461 | 46% helix, 16% strand | F9ULH8 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.76 | 0.82 | 54 | PO4 |
| 2 | 602 | 0.75 | 0.82 | 52 | PO4 |
| 3 | 579 | 0.75 | 0.82 | 46 | PO4 |
| 4 | 581 | 0.75 | 0.82 | 46 | PO4 |
| 5 | 594 | 0.75 | 0.82 | 37 | PO4 |
Interfaces
5 interfaces between chains.
- D–E · 743 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 736 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 733 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 351 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 112 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (artifact).
Compared structures
- 5NAQ · Crystal structure of native 6-phospho-glucosidase LpBgl from Lactobacillus plantarum · 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 F9ULH8
- Elsewhere: RCSB PDB 5NAQ · PDBe 5NAQ · UniProt F9ULH8
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