MolNFT v1 · #107611 · protein

Mouse galactocerebrosidase complexed with aza-galacto-fagomine agf

4UFI: “Mouse galactocerebrosidase complexed with aza-galacto-fagomine agf”. X-ray diffraction, 3 ligands (AGK, NAG, CA), 3 pockets (best druggability 0.48). MolNFT v1 #107611 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4UFI
Type: protein
Length: 641 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Galactocerebrosidase
EC: 3.2.1.46
UniProt: P54818
Ligands: AGK, NAG, CA
Pockets: 3 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Galactocerebrosidase (EC 3.2.1.46)	protein	641	18% helix, 34% strand	P54818

Ligands and binding sites

AGK · (3R,4S,5R)-3-(hydroxymethyl)-1,2-diazinane-4,5-diol · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
CA · Calcium ion · metal · chains A

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

Pockets

3 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	78	0.48	0.83	18	empty
2	120	0.37	0.73	21	empty
3	51	0.26	0.74	15	empty

Modifications

Observed in the structure: 4 glycan, 1 disulfide (N-glycosylation, disulfide).

Compared structures

4UFI · Mouse Galactocerebrosidase complexed with aza-galacto-fagomine AGF · the same entry in another collection · chain A against A, TM-score 1.00
P54818 · AlphaFold monomer V2.0 prediction for galactocerebrosidase (P54818) · a predicted model of the same protein · 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 P54818
Elsewhere: RCSB PDB 4UFI · PDBe 4UFI · UniProt P54818

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