MolNFT v1 · #37828 · protein
E232Q mutant of sucrose phosphorylase from bifidobacterium adolescentis in complex with sucrose
2GDU: “E232Q mutant of sucrose phosphorylase from bifidobacterium adolescentis in complex with sucrose”. X-ray diffraction, 2 ligands (GLC, FRU), 10 pockets (best druggability 0.78). MolNFT v1 #37828 on GenesisL1: 3D structure, binding…
- PDB
- 2GDU
- 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
- GLC, FRU
- Pockets
- 10 · best druggability 0.78
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
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.78 | 0.96 | 26 | GLC, FRU |
| 2 | 139 | 0.78 | 0.96 | 32 | GLC, FRU |
| 3 | 787 | 0.74 | 0.79 | 84 | empty |
| 4 | 294 | 0.60 | 0.78 | 34 | empty |
| 5 | 179 | 0.53 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 996 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 2GDU · E232Q mutant of sucrose phosphorylase from BIFIDOBACTERIUM ADOLESCENTIS in complex with… · the same entry in another collection · chain B against B, 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 2GDU · PDBe 2GDU · UniProt Q84HQ2
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