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Crystal structure of human alpha-galactosidase a in complex with 1- deoxygalactonojirimycin-pfpht

Analyse Crystal structure of human alpha-galactosidase a in complex with 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NXS
Type: protein
Length: 781 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-galactosidase a
EC: 3.2.1.22
UniProt: P06280
Ligands: 2OZ, NAG, SO4
Pockets: 6 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-galactosidase a (EC 3.2.1.22)	protein	390	28% helix, 24% strand	P06280
B	Alpha-galactosidase a (EC 3.2.1.22)	protein	391	29% helix, 25% strand	P06280

Ligands and binding sites

2OZ · (2R,3S,4R,5S)-N-(4-fluorophenyl)-3,4,5-trihydroxy-2-(hydroxymethyl)piperidine-1-carbothioamide · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
SO4 · Sulfate ion · ion · 5 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	317	0.56	0.76	45	empty
2	53	0.40	0.82	16	SO4
3	99	0.38	0.75	18	empty
4	106	0.37	0.75	18	empty
5	62	0.33	0.76	20	empty

Interfaces

1 interface between chains.

A–B · 978 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

4NXS · Crystal structure of human alpha-galactosidase A in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
P06280 · AlphaFold monomer V2.0 prediction for alpha-galactosidase a (P06280) · 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 P06280
Elsewhere: RCSB PDB 4NXS · PDBe 4NXS · UniProt P06280

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