Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclophellitol epoxide LWA481. Determined by X-ray diffraction at 2.02 Å resolution. Released 9 Oct 2019.
Explore 6IBR in 3D Show helices and sheets RCSB PDB PDBe
6IBR contains 33 α-helices and 48 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 | 117-126 | 10 | |
| β-strand | 130-136 | 7 | 1 |
| β-strand | 140 | 1 | 3 |
| β-strand | 146 | 1 | 3 |
| α-helix | 147 | 1 | |
| 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 | 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 |
| α-helix | 362 | 1 | |
| 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 |
| 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 | 176-193 | 18 | |
| β-strand | 199-202 | 4 | 7 |
| α-helix | 216-222 | 7 | |
| β-strand | 225-227 | 3 | 7 |
| 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 |
| β-strand | 348-355 | 8 | 11 |
| α-helix | 362 | 1 | |
| 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) |
>6IBR_1 Alpha-galactosidase A (chains A, B) LDNGLARTPTMGWLHWERFMCNLDCQEEPDSCISEKLFMEMAELMVSEGWKDAGYEYLCI DDCWMAPQRDSEGRLQADPQRFPHGIRQLANYVHSKGLKLGIYADVGNKTCAGFPGSFGY YDIDAQTFADWGVDLLKFDGCYCDSLENLADGYKHMSLALNRTGRSIVYSCEWPLYMWPF QKPNYTEIRQYCNHWRNFADIDDSWKSIKSILDWTSFNQERIVDVAGPGGWNDPDMLVIG NFGLSWNQQVTQMALWAIMAAPLFMSNDLRHISPQAKALLQDKDVIAINQDPLGKQGYQL RQGDNFEVWERPLSGLAWAVAMINRQEIGGPRSYTIAVASLGKGVACNPACFITQLLPVK RKLGFYEWTSRLRSHINPTGTVLLQLENTMQMSLKDLL
| ID | Name | Formula | Copies |
|---|---|---|---|
| HBE | (2~{R},3~{S},4~{S},5~{R},6~{S})-5-(hydroxymethyl)-7-oxabicyclo[4.1.0]heptane-2,… | C7 H12 O5 | 2 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
Water and common crystallization additives (SO4, EDO, PEG, ACT) are not listed.
Alpha-d-Gal-cyclophellitol cyclosulfamidate is a Michaelis complex analog that stabilizes therapeutic lysosomal alpha-galactosidase A in Fabry disease. Artola, M., Hedberg, C., Rowland, R.J. et al. Chem Sci (2019). DOI 10.1039/C9SC03342D
Other PDB entries of the same protein (UniProt P06280 (AlphaFold model), which also has an AlphaFold model), best resolution first:
MolViewer shows 6IBR directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.