3HG4: Alpha-galactosidase A

Human alpha-galactosidase catalytic mechanism 3. Covalent intermediate. Determined by X-ray diffraction at 2.3 Å resolution. Released 24 Nov 2009.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,250
Mol. weight: 95.51 kDa
Ligands: 7JZ, NAG, GAL
Released: 24 Nov 2009

Explore 3HG4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3HG4 contains 32 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: 15 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	152-161	10
β-strand	166-170	5	1
α-helix	177-193	17
β-strand	199-202	4	1
α-helix	204-208	5
α-helix	216-222	7
β-strand	225-227	3	1
α-helix	230-232	3
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	369-375	7
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	116-125	10
β-strand	130-136	7	7
β-strand	140	1	9
β-strand	146	1	9
α-helix	147	1
α-helix	152-161	10
β-strand	166-170	5	7
α-helix	177-192	16
β-strand	199-202	4	7
α-helix	204-208	5
α-helix	216-222	7
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	337-344	8	11
α-helix	345-347	3
β-strand	348-355	8	11
β-strand	363-368	6	12
α-helix	369-375	7
β-strand	381-388	8	11
β-strand	392-398	7	11
β-strand	402-407	6	12
β-strand	412-420	9	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

>3HG4_1 Alpha-galactosidase A (chains A, B)
LDNGLARTPTMGWLHWERFMCNLDCQEEPDSCISEKLFMEMAELMVSEGWKDAGYEYLCI
DDCWMAPQRDSEGRLQADPQRFPHGIRQLANYVHSKGLKLGIYADVGNKTCAGFPGSFGY
YDIDAQTFADWGVDLLKFDGCYCDSLENLADGYKHMSLALNRTGRSIVYSCEWPLYMWPF
QKPNYTEIRQYCNHWRNFADIDDSWKSIKSILDWTSFNQERIVDVAGPGGWNDPDMLVIG
NFGLSWNQQVTQMALWAIMAAPLFMSNDLRHISPQAKALLQDKDVIAINQDPLGKQGYQL
RQGDNFEVWERPLSGLAWAVAMINRQEIGGPRSYTIAVASLGKGVACNPACFITQLLPVK
RKLGFYEWTSRLRSHINPTGTVLLQLENTMQMSLKDLL

Ligands and cofactors

ID	Name	Formula	Copies
7JZ	2-deoxy-2,2-difluoro-beta-D-lyxo-hexopyranose	C6 H10 F2 O5	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
GAL	beta-D-galactopyranose	C6 H12 O6	1

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

Primary citation

Catalytic mechanism of human alpha-galactosidase. Guce, A.I., Clark, N.E., Salgado, E.N. et al. J Biol Chem (2010) 285:3625-3632. DOI 10.1074/jbc.M109.060145 · 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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