3GXP: Acid-alpha-galactosidase A

Crystal structure of acid-alpha-galactosidase A complexed with galactose at pH 4.5. Determined by X-ray diffraction at 2.2 Å resolution. Released 5 May 2009.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,666
Mol. weight: 94.78 kDa
Ligands: GLA, TAM, NAG, MAN
Released: 5 May 2009

Explore 3GXP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3GXP contains 33 α-helices and 47 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	42-45	4	1
α-helix	47-50	4
α-helix	66-78	13
β-strand	88-90	3	1
β-strand	96	1	2
β-strand	108	1	2
α-helix	116-126	11
β-strand	130-136	7	1
β-strand	140	1	3
β-strand	146	1	3
α-helix	147	1
α-helix	152-162	11
β-strand	166-170	5	1
α-helix	177-194	18
β-strand	199-202	4	1
α-helix	204-208	5
α-helix	216-222	7
β-strand	225-227	3	1
α-helix	236-248	13
α-helix	250-253	4
β-strand	258	1	4
β-strand	261	1	4
β-strand	262-264	3	1
β-strand	268	1	1
α-helix	277-289	13
β-strand	294-296	3	1
α-helix	305-311	7
α-helix	314-320	7
β-strand	329-334	6	5
β-strand	337-343	7	5
α-helix	345-347	3
β-strand	348-355	8	5
β-strand	363-368	6	6
α-helix	369-371	3
α-helix	373-375	3
β-strand	381-388	8	5
β-strand	392-398	7	5
β-strand	402-407	6	6
β-strand	409	1	5
β-strand	412-419	8	5

Chain B: 17 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	42-45	4	7
α-helix	47-50	4
α-helix	66-78	13
α-helix	81-84	4
β-strand	88-90	3	7
β-strand	96	1	8
β-strand	108	1	8
α-helix	116-126	11
β-strand	130-136	7	7
β-strand	140	1	9
β-strand	146	1	9
α-helix	152-162	11
β-strand	166-170	5	7
α-helix	177-192	16
β-strand	199-202	4	7
α-helix	204-208	5
α-helix	216-220	5
β-strand	225-227	3	7
α-helix	230-232	3
α-helix	236-248	13
α-helix	250-253	4
β-strand	258	1	10
β-strand	261	1	10
β-strand	262-264	3	7
β-strand	268	1	7
α-helix	277-289	13
β-strand	294-296	3	7
α-helix	305-311	7
α-helix	314-320	7
β-strand	329-334	6	11
β-strand	337-343	7	11
α-helix	345-347	3
β-strand	349-355	7	11
β-strand	363-368	6	12
α-helix	369-371	3
α-helix	373-375	3
β-strand	381-388	8	11
β-strand	392-398	7	11
β-strand	402-407	6	12
β-strand	412-419	8	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alpha-galactosidase A	A, B	protein	398	Homo sapiens	P06280 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3GXP_1 Alpha-galactosidase A (chains A, B)
LDNGLARTPTMGWLHWERFMCNLDCQEEPDSCISEKLFMEMAELMVSEGWKDAGYEYLCI
DDCWMAPQRDSEGRLQADPQRFPHGIRQLANYVHSKGLKLGIYADVGNKTCAGFPGSFGY
YDIDAQTFADWGVDLLKFDGCYCDSLENLADGYKHMSLALNRTGRSIVYSCEWPLYMWPF
QKPNYTEIRQYCNHWRNFADIDDSWKSIKSILDWTSFNQERIVDVAGPGGWNDPDMLVIG
NFGLSWNQQVTQMALWAIMAAPLFMSNDLRHISPQAKALLQDKDVIAINQDPLGKQGYQL
RQGDNFEVWERPLSGLAWAVAMINRQEIGGPRSYTIAVASLGKGVACNPACFITQLLPVK
RKLGFYEWTSRLRSHINPTGTVLLQLENTMQMSLKDLL

Ligands and cofactors

ID	Name	Formula	Copies
GLA	alpha-D-galactopyranose	C6 H12 O6	2
TAM	Tris(hydroxyethyl)aminomethane	C7 H17 N O3	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
MAN	alpha-D-mannopyranose	C6 H12 O6	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Effects of pH and iminosugar pharmacological chaperones on lysosomal glycosidase structure and stability. Lieberman, R.L., D'aquino, J.A., Ringe, D. et al. Biochemistry (2009) 48:4816-4827. DOI 10.1021/bi9002265 · PubMed

Other PDB entries of the same protein (UniProt P06280 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3HG3 1.9 Å, Human alpha-galactosidase catalytic mechanism 2. Substrate bound
8K7F 1.98 Å, Crystal structure of human lysosomal alpha-galactosidase A in complex with…
6IBK 1.99 Å, Crystal structure of human alpha-galactosidase A in complex with alpha-galactose…
8K7K 2.0 Å, Crystal structure of human lysosomal alpha-galactosidase A in complex with…
8K7L 2.0 Å, Crystal structure of human lysosomal alpha-galactosidase A in complex with…
3S5Z 2.0 Å, Pharmacological Chaperoning in Human alpha-Galactosidase
8K7J 2.01 Å, Crystal structure of human lysosomal alpha-galactosidase A in complex with…
6IBR 2.02 Å, Crystal structure of human alpha-galactosidase A in complex with alpha-galactose…
3LX9 2.04 Å, Interconversion of Human Lysosomal Enzyme Specificities
6IBT 2.04 Å, Crystal structure of human alpha-galactosidase A in complex with alpha-galactose…
6IBM 2.07 Å, Crystal structure of human alpha-galactosidase A in complex with alpha-galactose…
3S5Y 2.1 Å, Pharmacological Chaperoning in Human alpha-Galactosidase

Browse structure collections

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