MolNFT v1 · #66088 · protein

Human alpha-galactosidase catalytic mechanism 2. substrate bound

3HG3 · Alpha-galactosidase a: “Human alpha-galactosidase catalytic mechanism 2. substrate bound”. X-ray diffraction, 5 ligands (NAG, BMA, MAN), 5 pockets (best druggability 0.50). MolNFT v1 #66088 on GenesisL1: 3D structure, binding sites…

PDB: 3HG3
Type: protein
Length: 789 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, MAN, GLC, GLA
Pockets: 5 · best druggability 0.50

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-galactosidase a (EC 3.2.1.22)	protein	395	32% helix, 24% strand	P06280
B	Alpha-galactosidase a (EC 3.2.1.22)	protein	394	32% helix, 24% strand	P06280

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 2 copies
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
GLA · alpha-D-galactopyranose · sugar · 2 copies · chains A, B
2PE · Nonaethylene glycol · additive · 5 copies · chains A, B

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

Pockets

5 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	286	0.50	0.74	37	2PE
2	69	0.46	0.82	15	empty
3	128	0.42	0.76	22	empty
4	126	0.41	0.76	21	empty
5	51	0.40	0.82	18	GLC, GLA

Interfaces

1 interface between chains.

A–B · 1094 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

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

Compared structures

3HG3 · Human alpha-galactosidase catalytic mechanism 2. Substrate bound · the same entry in another collection · chain B against B, TM-score 1.00
P06280 · AlphaFold monomer V2.0 prediction for alpha-galactosidase a (P06280) · a predicted model of the same protein · chain B 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 3HG3 · PDBe 3HG3 · UniProt P06280

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