MolNFT v1 · #55284 · protein

Galactosidase domain of alpha-galactosidase-sucrose kinase, agask

2YFN · Alpha-galactosidase-sucrose kinase agask: “Galactosidase domain of alpha-galactosidase-sucrose kinase, agask”. X-ray diffraction, 2 ligands (MG, PO4), 5 pockets (best druggability 0.48). MolNFT v1 #55284 on GenesisL1: 3D structure…

PDB: 2YFN
Type: protein
Length: 719 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-galactosidase-sucrose kinase agask
EC: 3.2.1.22
Ligands: MG, PO4
Pockets: 5 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-galactosidase-sucrose kinase agask (EC 3.2.1.22)	protein	719	22% helix, 33% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A
PO4 · Phosphate ion · ion · chains A
GOL · Glycerol · additive · 2 copies · chains A
EDO · 1,2-ethanediol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	176	0.48	0.77	29	empty
2	99	0.48	0.81	18	GOL
3	129	0.48	0.79	31	empty
4	137	0.42	0.75	26	empty
5	50	0.34	0.79	13	empty

Compared structures

2YFN · galactosidase domain of alpha-galactosidase-sucrose kinase, AgaSK · 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
Elsewhere: RCSB PDB 2YFN · PDBe 2YFN

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