Research workbench
The complex structure of beta-1,2-glucosyltransferase from ignavibacterium album with P-nitrophenyl-alpha-D-glucopyranoside
Analyse The complex structure of beta-1,2-glucosyltransferase from ignavibacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VL0
- Type
- protein
- Length
- 1,409 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- UniProt
- I0AIT9
- Ligands
- PNG, CA
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactosidase | protein | 706 | 35% helix, 24% strand | I0AIT9 |
| B | Beta-galactosidase | protein | 703 | 36% helix, 24% strand | I0AIT9 |
Ligands and binding sites
- PNG · 4-nitrophenyl alpha-D-glucopyranoside · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 471 | 0.77 | 0.85 | 80 | PNG |
| 2 | 97 | 0.72 | 0.94 | 23 | empty |
| 3 | 261 | 0.72 | 0.87 | 40 | PNG |
| 4 | 54 | 0.71 | 0.98 | 22 | empty |
| 5 | 341 | 0.66 | 0.81 | 55 | empty |
Interfaces
1 interface between chains.
- A–B · 1907 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 7VL0 · The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with… · 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 I0AIT9
- Elsewhere: RCSB PDB 7VL0 · PDBe 7VL0 · UniProt I0AIT9
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