MolNFT v1 · #161960 · protein

2-deoxy-galactose reaction intermediate of a truncated beta- galactosidase III from bifidobacterium bifidum

6QUD · Beta-galactosidase: “2-deoxy-galactose reaction intermediate of a truncated beta- galactosidase III from bifidobacterium bifidum”. X-ray diffraction, 2 ligands (2DG, CA), 12 pockets (best druggability 0.75). MolNFT v1 #161960 on…

PDB: 6QUD
Type: protein
Length: 837 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-galactosidase
EC: 3.2.1.23
UniProt: Q9F4D5
Ligands: 2DG, CA
Pockets: 12 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-galactosidase (EC 3.2.1.23)	protein	837	14% helix, 39% strand	Q9F4D5

Ligands and binding sites

2DG · 2-deoxy-alpha-D-galactopyranose · ligand · chains A
CA · Calcium ion · metal · chains A

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

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1166	0.75	0.78	108	empty
2	455	0.67	0.79	46	empty
3	124	0.63	0.87	20	empty
4	336	0.60	0.77	42	empty
5	125	0.48	0.79	28	empty

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

6QUD · 2-deoxy-galactose reaction intermediate of a Truncated beta-galactosidase III from… · 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 Q9F4D5
Elsewhere: RCSB PDB 6QUD · PDBe 6QUD · UniProt Q9F4D5

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