Research workbench
Sucrose phosphorylase from bifidobacterium adolescentis reacted with sucrose
Analyse Sucrose phosphorylase from bifidobacterium adolescentis reacted with sucrose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GDV
- Type
- protein
- Length
- 1,008 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sucrose phosphorylase
- EC
- 2.4.1.7
- UniProt
- Q84HQ2
- Ligands
- BGC
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sucrose phosphorylase (EC 2.4.1.7) | protein | 504 | 38% helix, 20% strand | Q84HQ2 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.77 | 0.80 | 78 | empty |
| 2 | 115 | 0.77 | 0.97 | 26 | BGC |
| 3 | 59 | 0.68 | 0.96 | 17 | BGC |
| 4 | 194 | 0.55 | 0.79 | 22 | empty |
| 5 | 100 | 0.40 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1127 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 glycan (glycosylation).
Compared structures
- 2GDV · Sucrose phosphorylase from BIFIDOBACTERIUM ADOLESCENTIS reacted with sucrose · 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 Q84HQ2
- Elsewhere: RCSB PDB 2GDV · PDBe 2GDV · UniProt Q84HQ2
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