Research workbench

Crystal structure of human gaa

Analyse Crystal structure of human gaa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KZW
Type: protein
Length: 850 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysosomal alpha-glucosidase
EC: 3.2.1.20
UniProt: P10253
Ligands: NAG, FCA, GLC, BGC, BMA, SO4
Pockets: 12 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysosomal alpha-glucosidase (EC 3.2.1.20)	protein	850	22% helix, 30% strand	P10253

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A
FCA · alpha-D-fucopyranose · sugar · 2 copies · chains A
GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
BGC · beta-D-glucopyranose · sugar · 2 copies · chains A
BMA · beta-D-mannopyranose · sugar
SO4 · Sulfate ion · ion · 3 copies · chains A
EDO · 1,2-ethanediol · additive · 3 copies · chains A
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
PGE · Triethylene glycol · additive · 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	174	0.58	0.81	27	empty
2	75	0.53	0.86	17	empty
3	95	0.51	0.82	20	GLC, BGC
4	98	0.50	0.82	23	empty
5	185	0.50	0.77	21	SO4

Modifications

Observed in the structure: 6 glycan, 5 disulfide (N-glycosylation, disulfide).

Compared structures

5KZW · Crystal structure of human GAA · the same entry in another collection · chain A against A, TM-score 1.00
P10253 · AlphaFold monomer V2.0 prediction for lysosomal alpha-glucosidase (P10253) · 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 P10253
Elsewhere: RCSB PDB 5KZW · PDBe 5KZW · UniProt P10253

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