MolNFT v1 · #126699 · protein
Structure of sucrose phosphorylase from bifidobacterium adolescentis bound to nigerose
5MAN: “Structure of sucrose phosphorylase from bifidobacterium adolescentis bound to nigerose”. X-ray diffraction, 1 ligand (GLC), 3 pockets (best druggability 0.73). MolNFT v1 #126699 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5MAN
- Type
- protein
- Length
- 504 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sucrose phosphorylase
- EC
- 2.4.1.7
- UniProt
- Q84HQ2
- Ligands
- GLC
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Sucrose phosphorylase (EC 2.4.1.7) | protein | 504 | 37% helix, 20% strand | Q84HQ2 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.73 | 0.85 | 43 | GLC |
| 2 | 74 | 0.41 | 0.79 | 20 | empty |
| 3 | 52 | 0.35 | 0.79 | 21 | empty |
Compared structures
- 5MAN · Structure of sucrose phosphorylase from Bifidobacterium adolescentis bound to nigerose · 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 5MAN · PDBe 5MAN · UniProt Q84HQ2
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