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Human alpha-galactosidase catalytic mechanism 4. product bound

Analyse Human alpha-galactosidase catalytic mechanism 4. product bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3HG5
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: NAG, BMA, GLA, MAN, GAL, SO4
Pockets: 2 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-galactosidase a (EC 3.2.1.22)	protein	390	32% helix, 24% strand	P06280
B	Alpha-galactosidase a (EC 3.2.1.22)	protein	391	31% helix, 24% strand	P06280

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 2 copies
GLA · alpha-D-galactopyranose · sugar · 2 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · chains B
GAL · beta-D-galactopyranose · sugar · chains B
SO4 · Sulfate ion · ion · 4 copies · chains A, B
ACY · Acetic acid · additive · 4 copies · chains A, B

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

Pockets

2 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	574	0.64	0.76	83	ACY
2	56	0.39	0.81	15	empty

Interfaces

1 interface between chains.

A–B · 958 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

3HG5 · Human alpha-galactosidase catalytic mechanism 4. Product bound · 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 3HG5 · PDBe 3HG5 · UniProt P06280

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