MolNFT v1 · #51305 · protein

Acid-beta-glucosidase produced in carrot

2V3F · Glucosylceramidase: “Acid-beta-glucosidase produced in carrot”. X-ray diffraction, 4 ligands (NAG, FUC, MAN), 11 pockets (best druggability 0.87). MolNFT v1 #51305 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2V3F
Type: protein
Length: 986 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucosylceramidase
EC: 3.2.1.45
UniProt: P04062
Ligands: NAG, FUC, MAN, SO4
Pockets: 11 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucosylceramidase (EC 3.2.1.45)	protein	496	28% helix, 27% strand	P04062
B	Glucosylceramidase (EC 3.2.1.45)	protein	490	28% helix, 28% strand	P04062

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
FUC · alpha-L-fucopyranose · sugar · 2 copies
MAN · alpha-D-mannopyranose · sugar
SO4 · Sulfate ion · ion · 12 copies · chains A, B
BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B

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

Pockets

11 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	631	0.87	0.91	55	BTB
2	437	0.68	0.80	41	SO4
3	429	0.67	0.79	41	SO4
4	200	0.64	0.84	28	empty
5	78	0.49	0.83	24	SO4

Interfaces

1 interface between chains.

A–B · 1021 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

2V3F · acid-beta-glucosidase produced in carrot · the same entry in another collection · chain A against A, TM-score 1.00
P04062 · AlphaFold monomer V2.0 prediction for lysosomal acid glucosylceramidase (P04062) · 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 P04062
Elsewhere: RCSB PDB 2V3F · PDBe 2V3F · UniProt P04062

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.