Subatomic crystal structure of glucose isomerase from Streptomyces rubiginosus. Determined by X-ray diffraction at 0.99 Å resolution. Released 4 Oct 2023.
Explore 8WDG in 3D Show helices and sheets RCSB PDB PDBe
8WDG contains 23 α-helices and 20 β-strands across 1 chain. 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 |
|---|---|---|---|
| α-helix | 7-9 | 3 | |
| β-strand | 11-14 | 4 | 1 |
| α-helix | 15-18 | 4 | |
| β-strand | 24 | 1 | 2 |
| β-strand | 27 | 1 | 2 |
| α-helix | 32-35 | 4 | |
| α-helix | 36-46 | 11 | |
| β-strand | 50-52 | 3 | 1 |
| β-strand | 53-54 | 2 | 3 |
| α-helix | 55-58 | 4 | |
| α-helix | 65-82 | 18 | |
| β-strand | 85 | 1 | 1 |
| β-strand | 88-90 | 3 | 3 |
| α-helix | 97-99 | 3 | |
| α-helix | 109-128 | 20 | |
| β-strand | 133-136 | 4 | 3 |
| β-strand | 142-143 | 2 | 4 |
| α-helix | 146-148 | 3 | |
| α-helix | 151-171 | 21 | |
| β-strand | 177-180 | 4 | 3 |
| β-strand | 190-191 | 2 | 4 |
| α-helix | 196-203 | 8 | |
| α-helix | 209-211 | 3 | |
| β-strand | 212-214 | 3 | 3 |
| β-strand | 217 | 1 | 1 |
| α-helix | 218-222 | 5 | |
| α-helix | 228-237 | 10 | |
| β-strand | 241 | 1 | 3 |
| β-strand | 245-246 | 2 | 1 |
| β-strand | 248 | 1 | 5 |
| β-strand | 258 | 1 | 5 |
| α-helix | 259 | 1 | |
| β-strand | 260 | 1 | 6 |
| β-strand | 262 | 1 | 6 |
| α-helix | 265-277 | 13 | |
| β-strand | 284-286 | 3 | 1 |
| α-helix | 296-322 | 27 | |
| α-helix | 324-332 | 9 | |
| α-helix | 335-338 | 4 | |
| α-helix | 347-352 | 6 | |
| α-helix | 354-356 | 3 | |
| α-helix | 362-367 | 6 | |
| α-helix | 372-384 | 13 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Xylose isomerase | A | protein | 385 | Streptomyces rubiginosus | P24300 (AlphaFold model) |
>8WDG_1 Xylose isomerase (chains A) YQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFG SSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRN IDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEP KPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLF HIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWAS AAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDV DAAAARGMAFERLDQLAMDHLLGAR
Xylitol binding to the M1 site of glucose isomerase induces a conformational change in the substrate binding channel. Xu, Y., Nam, K.H. Biochem Biophys Res Commun (2023) 682:21-26. DOI 10.1016/j.bbrc.2023.09.087 · PubMed
Other PDB entries of the same protein (UniProt P24300 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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