Crystal structure of human lysosomal alpha-galactosidase A in complex with (2R,3R,4S,5R)-2-((dimethylamino)methyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol. Determined by X-ray diffraction at 2.01 Å resolution. Released 10 Apr 2024.
Explore 8K7J in 3D Show helices and sheets RCSB PDB PDBe
8K7J contains 36 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 42-45 | 4 | 1 |
| α-helix | 47-50 | 4 | |
| α-helix | 66-78 | 13 | |
| α-helix | 81-84 | 4 | |
| 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 | 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 |
| 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 | 412-419 | 8 | 5 |
| α-helix | 420-422 | 3 |
| 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 | 147 | 1 | |
| α-helix | 152-162 | 11 | |
| β-strand | 166-170 | 5 | 7 |
| α-helix | 177-194 | 18 | |
| 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 | 337-343 | 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 | 409 | 1 | 11 |
| β-strand | 412-420 | 9 | 11 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Alpha-galactosidase A | A, B | protein | 398 | Homo sapiens | P06280 (AlphaFold model) |
>8K7J_1 Alpha-galactosidase A (chains A, B) LDNGLARTPTMGWLHWERFMCNLDCQEEPDSCISEKLFMEMAELMVSEGWKDAGYEYLCI DDCWMAPQRDSEGRLQADPQRFPHGIRQLANYVHSKGLKLGIYADVGNKTCAGFPGSFGY YDIDAQTFADWGVDLLKFDGCYCDSLENLADGYKHMSLALNRTGRSIVYSCEWPLYMWPF QKPNYTEIRQYCNHWRNFADIDDSWKSIKSILDWTSFNQERIVDVAGPGGWNDPDMLVIG NFGLSWNQQVTQMALWAIMAAPLFMSNDLRHISPQAKALLQDKDVIAINQDPLGKQGYQL RQGDNFEVWERPLSGLAWAVAMINRQEIGGPRSYTIAVASLGKGVACNPACFITQLLPVK RKLGFYEWTSRLRSHINPTGTVLLQLENTMQMSLKDLL
| ID | Name | Formula | Copies |
|---|---|---|---|
| VNB | (2~{R},3~{R},4~{S},5~{R})-2-[(dimethylamino)methyl]-5-(hydroxymethyl)pyrrolidin… | C8 H18 N2 O3 | 2 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
Water and common crystallization additives (P6G, SO4) are not listed.
Mechanistic Insights into Dibasic Iminosugars as pH-Selective Pharmacological Chaperones to Stabilize Human alpha-Galactosidase. Li, H.Y., Lin, H.Y., Chang, S.K. et al. JACS Au (2024) 4:908-918. DOI 10.1021/jacsau.3c00684 · PubMed
Other PDB entries of the same protein (UniProt P06280 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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