9AVS: Human alpha-galactosidase A

Human alpha-galactosidase A in complex with saposin B. Determined by X-ray diffraction at 3.53 Å resolution. Released 17 Apr 2024.

Method
X-ray diffraction
Resolution
3.53 Å
Organism
Homo sapiens
Chains
3
Atoms
7,159
Mol. weight
108.5 kDa
Ligands
NAG
Released
17 Apr 2024

Explore 9AVS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9AVS contains 35 α-helices and 47 β-strands across 3 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: 14 helices, 25 β-strands

ElementResiduesLengthSheet
β-strand43-4421
α-helix47-504
α-helix66-7813
α-helix81-844
β-strand88-8921
β-strand9612
β-strand10812
α-helix117-12610
β-strand130-13121
β-strand132-13653
β-strand14014
β-strand14614
α-helix152-16211
β-strand166-17053
α-helix177-19216
β-strand199-20243
α-helix216-2227
β-strand225-22733
α-helix231-2322
α-helix236-24813
α-helix250-2534
β-strand25815
β-strand26115
β-strand262-26433
β-strand26811
α-helix277-28913
β-strand295-29621
α-helix305-3117
α-helix314-3207
β-strand329-33466
β-strand337-34486
β-strand348-35586
β-strand363-36867
α-helix369-3757
β-strand381-38886
β-strand392-39876
β-strand402-40767
β-strand40916
β-strand411-41776
Chain B: 15 helices, 22 β-strands
ElementResiduesLengthSheet
β-strand42-4438
α-helix66-7813
α-helix81-844
β-strand88-8928
β-strand9619
β-strand10819
α-helix117-12610
β-strand130-13128
β-strand132-136510
β-strand140111
β-strand146111
α-helix152-16211
β-strand166-170510
α-helix177-19418
β-strand199-202410
α-helix204-2085
α-helix216-2227
β-strand225-227310
α-helix236-24813
α-helix250-2534
β-strand262-264310
β-strand26818
α-helix277-28913
β-strand294-29638
α-helix305-3117
α-helix314-3207
α-helix326-3283
β-strand329-334612
β-strand337-343712
β-strand348-355812
β-strand363-368613
α-helix369-3713
α-helix373-3753
β-strand381-388812
β-strand392-398712
β-strand402-407613
β-strand411-418812
Chain C: 6 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix5-1915
α-helix25-3511
α-helix36-394
α-helix44-529
α-helix56-649
α-helix67-748

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Alpha-galactosidase AA, Bprotein414Homo sapiensP06280 (AlphaFold model)
Saposin-BCprotein82Homo sapiensP07602 (AlphaFold model)
Sequence of entity 1 (A, B), FASTA
>9AVS_1 Alpha-galactosidase A (chains A, B)
LDNGLARTPTMGWLHWERFMCNLDCQEEPDSCISEKLFMEMAELMVSEGWKDAGYEYLCI
DDCWMAPQRDSEGRLQADPQRFPHGIRQLANYVHSKGLKLGIYADVGNKTCAGFPGSFGY
YDIDAQTFADWGVDLLKFAGCYCDSLENLADGYKHMSLALNRTGRSIVYSCEWPLYMWPF
QKPNYTEIRQYCNHWRNFADIDDSWKSIKSILDWTSFNQERIVDVAGPGGWNDPDMLVIG
NFGLSWNQQVTQMALWAIMAAPLFMSNDLRHISPQAKALLQDKDVIAINQDPLGKQGYQL
RQGDNFEVWERPLSGLAWAVAMINRQEIGGPRSYTIAVASLGKGVACNPACFITQLLPVK
RKLGFYEWTSRLRSHINPTGTVLLQLENTMQMSLKDLLDYKDDDDKDYKDDDDK
Sequence of entity 2 (C), FASTA
>9AVS_2 Saposin-B (chains C)
GASGDVCQDCIQMVTDIQTAVRTNSTFVQALVEHVKEECDRLGPGMADICKNYISQYSEI
AIQMMMHMQPKEICALVGFCDE

Ligands and cofactors

IDNameFormulaCopies
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O61

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

Primary citation

Human Saposin B Ligand Binding and Presentation to alpha-Galactosidase A. Sawyer, T.K., Aral, E., Staros, J.V. et al. bioRxiv (2024). DOI 10.1101/2024.04.04.584535 · PubMed

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

Browse structure collections

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