MolNFT v1 · #53101 · protein

Velaglucerase alfa

2WKL · Glucosylceramidase: “Velaglucerase alfa”. X-ray diffraction, 2 ligands (NAG, SO4), 6 pockets (best druggability 0.82). MolNFT v1 #53101 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2WKL
Type: protein
Length: 992 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, SO4
Pockets: 6 · best druggability 0.82

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucosylceramidase (EC 3.2.1.45)	protein	495	27% helix, 28% strand	P04062
B	Glucosylceramidase (EC 3.2.1.45)	protein	497	27% helix, 28% strand	P04062

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
SO4 · Sulfate ion · ion · 18 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1087	0.82	0.83	92	empty
2	262	0.67	0.83	39	SO4
3	149	0.51	0.79	21	SO4
4	89	0.43	0.79	25	empty
5	67	0.31	0.74	19	empty

Interfaces

1 interface between chains.

A–B · 605 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

2WKL · Velaglucerase alfa · 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 0.99

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 2WKL · PDBe 2WKL · UniProt P04062

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