Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes. Determined by X-ray diffraction at 1.52 Å resolution. Released 27 Nov 2019.
Explore 6S8K in 3D Show helices and sheets RCSB PDB PDBe
6S8K contains 68 α-helices and 37 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 4-9 | 6 | 1 |
| α-helix | 10-28 | 19 | |
| α-helix | 48-51 | 4 | |
| β-strand | 53-55 | 3 | 2 |
| β-strand | 61-63 | 3 | 2 |
| β-strand | 65-69 | 5 | 1 |
| α-helix | 73-80 | 8 | |
| α-helix | 89-91 | 3 | |
| β-strand | 92-94 | 3 | 1 |
| α-helix | 103-104 | 2 | |
| α-helix | 105-109 | 5 | |
| α-helix | 111-113 | 3 | |
| α-helix | 115-127 | 13 | |
| β-strand | 134-140 | 7 | 1 |
| α-helix | 144 | 1 | |
| α-helix | 145-149 | 5 | |
| α-helix | 150-160 | 11 | |
| β-strand | 165-172 | 8 | 1 |
| α-helix | 175-177 | 3 | |
| α-helix | 183-194 | 12 | |
| α-helix | 195-197 | 3 | |
| β-strand | 200-205 | 6 | 1 |
| α-helix | 206-215 | 10 | |
| α-helix | 224-243 | 20 | |
| α-helix | 252-259 | 8 | |
| α-helix | 268 | 1 | |
| β-strand | 269-273 | 5 | 3 |
| β-strand | 277 | 1 | 4 |
| α-helix | 283-287 | 5 | |
| α-helix | 288-294 | 7 | |
| α-helix | 298-300 | 3 | |
| β-strand | 301 | 1 | 3 |
| α-helix | 307-309 | 3 | |
| β-strand | 312-321 | 10 | 3 |
| α-helix | 325-338 | 14 | |
| α-helix | 342 | 1 | |
| β-strand | 343 | 1 | 3 |
| α-helix | 344 | 1 | |
| α-helix | 350-351 | 2 | |
| β-strand | 352-356 | 5 | 3 |
| α-helix | 359-361 | 3 | |
| β-strand | 368 | 1 | 4 |
| α-helix | 369-370 | 2 | |
| β-strand | 373-381 | 9 | 3 |
| α-helix | 382-384 | 3 | |
| α-helix | 385-399 | 15 | |
| α-helix | 405-409 | 5 | |
| α-helix | 416-436 | 21 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 4-9 | 6 | 5 |
| α-helix | 10-28 | 19 | |
| β-strand | 30 | 1 | 6 |
| β-strand | 35 | 1 | 7 |
| β-strand | 36 | 1 | 6 |
| α-helix | 42-47 | 4 | |
| α-helix | 49-51 | 3 | |
| β-strand | 53-55 | 3 | 8 |
| β-strand | 60 | 1 | 7 |
| β-strand | 61-63 | 3 | 8 |
| β-strand | 65-69 | 5 | 5 |
| α-helix | 72-80 | 9 | |
| α-helix | 84-86 | 3 | |
| α-helix | 89-91 | 3 | |
| β-strand | 92-94 | 3 | 5 |
| α-helix | 103-108 | 6 | |
| α-helix | 110-127 | 18 | |
| β-strand | 134-140 | 7 | 5 |
| α-helix | 145-149 | 5 | |
| α-helix | 150-160 | 11 | |
| β-strand | 165-172 | 8 | 5 |
| α-helix | 173 | 1 | |
| β-strand | 174 | 1 | 9 |
| β-strand | 177 | 1 | 9 |
| α-helix | 183-197 | 15 | |
| β-strand | 200-205 | 6 | 5 |
| α-helix | 206-211 | 6 | |
| α-helix | 212-216 | 5 | |
| α-helix | 224-243 | 20 | |
| α-helix | 252-259 | 8 | |
| β-strand | 267-268 | 2 | 5 |
| β-strand | 269-273 | 5 | 10 |
| α-helix | 285-287 | 3 | |
| α-helix | 288-296 | 9 | |
| α-helix | 298-300 | 3 | |
| β-strand | 301 | 1 | 10 |
| α-helix | 307-309 | 3 | |
| β-strand | 312-321 | 10 | 10 |
| α-helix | 325-338 | 14 | |
| α-helix | 340-342 | 3 | |
| β-strand | 343 | 1 | 10 |
| β-strand | 351-356 | 6 | 10 |
| β-strand | 373-381 | 9 | 10 |
| α-helix | 382-384 | 3 | |
| α-helix | 385-400 | 16 | |
| α-helix | 406-409 | 4 | |
| α-helix | 415-436 | 22 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 14-24 | 11 | |
| α-helix | 27-35 | 9 | |
| α-helix | 50-57 | 8 | |
| α-helix | 60-68 | 9 | |
| α-helix | 83-90 | 8 | |
| α-helix | 93-101 | 9 | |
| α-helix | 116-122 | 7 | |
| α-helix | 126-134 | 9 | |
| α-helix | 149-155 | 7 | |
| α-helix | 159-165 | 7 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Tubulin alpha-1B chain | A | protein | 437 | Bos taurus | P81947 (AlphaFold model) |
| Tubulin beta-2B chain | B | protein | 445 | Bos taurus | Q6B856 (AlphaFold model) |
| Designed ankyrin repeat protein (DARPIN) D1 | F | protein | 155 | synthetic construct |
>6S8K_1 Tubulin alpha-1B chain (chains A) MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE AREDMAALEKDYEEVGV
>6S8K_2 Tubulin beta-2B chain (chains B) MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS EYQQYQDATADEQGEFEEEEGEDEA
>6S8K_3 Designed ankyrin repeat protein (DARPIN) D1 (chains F) DLGKKLLEAARAGQDDEVRILMANGADVNATDASGLTPLHLAATYGHLEIVEVLLKHGAD VNAIDIMGSTPLHLAALIGHLEIVEVLLKHGADVNAVDTWGDTPLHLAAIMGHLEIVEVL LKHGADVNAQDKFGKTAFDISIDNGNEDLAEILQK
| ID | Name | Formula | Copies |
|---|---|---|---|
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 1 |
| PN6 | (3Z,6Z)-3-benzylidene-6-[(5-tert-butyl-1H-imidazol-4-yl)methylidene]piperazine-… | C19 H20 N4 O2 | 1 |
| MG | Magnesium ion | Mg | 1 |
| GTP | Guanosine-5'-triphosphate | C10 H16 N5 O14 P3 | 1 |
Structure, Thermodynamics, and Kinetics of Plinabulin Binding to Two Tubulin Isotypes. La Sala, G., Olieric, N., Sharma, A. Chem (2019) 5. DOI 10.1016/j.chempr.2019.08.022
Other PDB entries of the same protein (UniProt P81947 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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