Structure of PP5C with LB-100; 7-oxabicyclo[2.2.1]heptane-2,3-dicarbonyl moiety modeled in the density. Determined by X-ray diffraction at 1.65 Å resolution. Released 18 Jul 2018.
Explore 5WG8 in 3D Show helices and sheets RCSB PDB PDBe
5WG8 contains 13 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 |
|---|---|---|---|
| β-strand | 182 | 1 | 1 |
| β-strand | 185 | 1 | 1 |
| α-helix | 188-199 | 12 | |
| α-helix | 206-221 | 16 | |
| β-strand | 226-229 | 4 | 2 |
| β-strand | 236-240 | 5 | 3 |
| β-strand | 242 | 1 | 4 |
| α-helix | 247-257 | 11 | |
| β-strand | 261 | 1 | 5 |
| β-strand | 264 | 1 | 5 |
| β-strand | 266-269 | 4 | 3 |
| α-helix | 279-292 | 14 | |
| β-strand | 297-300 | 4 | 3 |
| α-helix | 307-313 | 7 | |
| α-helix | 315-322 | 8 | |
| α-helix | 325-335 | 11 | |
| β-strand | 341-344 | 4 | 2 |
| β-strand | 348-351 | 4 | 2 |
| α-helix | 363-367 | 5 | |
| α-helix | 374-376 | 3 | |
| α-helix | 380-386 | 7 | |
| β-strand | 388-389 | 2 | 6 |
| β-strand | 395-397 | 3 | 6 |
| β-strand | 404-406 | 3 | 6 |
| α-helix | 408-418 | 11 | |
| β-strand | 422-425 | 4 | 2 |
| β-strand | 434-437 | 4 | 2 |
| α-helix | 438-440 | 3 | |
| β-strand | 442-445 | 4 | 2 |
| β-strand | 446 | 1 | 4 |
| α-helix | 451-453 | 3 | |
| β-strand | 459-465 | 7 | 3 |
| β-strand | 468-476 | 9 | 3 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Serine/threonine-protein phosphatase 5 | A | protein | 333 | Homo sapiens | P53041 (AlphaFold model) |
>5WG8_1 Serine/threonine-protein phosphatase 5 (chains A) GASMTIEDEYSGPKLEDGKVTISFMKELMQWYKDQKKLHRKCAYQILVQVKEVLSKLSTL VETTLKETEKITVCGDTHGQFYDLLNIFELNGLPSETNPYIFNGDFVDRGSFSVEVILTL FGFKLLYPDHFHLLRGNHETDNMNQIYGFEGEVKAKYTAQMYELFSEVFEWLPLAQCING KVLIMHGGLFSEDGVTLDDIRKIERNRQPPDSGPMCDLLWSDPQPQNGRSISKRGVSCQF GPDVTKAFLEENNLDYIIRSHEVKAEGYEVAHGGRCVTVFSAPNYCDQMGNKASYIHLQG SDLRPQFHQFTAVPHPNVKPMAYANTLLQLGMM
| ID | Name | Formula | Copies |
|---|---|---|---|
| MN | Manganese (II) ion | Mn | 2 |
| LB1 | (1S,2R,3S,4R)-3-(4-methylpiperazine-1-carbonyl)-7-oxabicyclo[2.2.1]heptane-2-ca… | C13 H20 N2 O4 | 1 |
| MRD | (4R)-2-methylpentane-2,4-diol | C6 H14 O2 | 1 |
Water and common crystallization additives (MPD) are not listed.
The Antitumor Drug LB-100 Is a Catalytic Inhibitor of Protein Phosphatase 2A (PPP2CA) and 5 (PPP5C) Coordinating with the Active-Site Catalytic Metals in PPP5C. D'Arcy, B.M., Swingle, M.R., Papke, C.M. et al. Mol Cancer Ther (2019) 18:556-566. DOI 10.1158/1535-7163.MCT-17-1143 · PubMed
Other PDB entries of the same protein (UniProt P53041 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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