9GMY: Tubulin
Tubulin in complex with an oxathiane analog of zampanolide. Determined by X-ray diffraction at 1.97 Å resolution. Released 10 Sept 2025.
- Method
- X-ray diffraction
- Resolution
- 1.97 Å
- Organisms
- Bos taurus, Rattus norvegicus, Gallus gallus
- Chains
- 6
- Atoms
- 18,956
- Mol. weight
- 271.08 kDa
- Ligands
- GTP, MG, CA, GDP
- Released
- 10 Sept 2025
Explore 9GMY in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9GMY contains 126 α-helices and 90 β-strands across 6 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.
Chain A: 28 helices, 16 β-strands
| 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 | 84-86 | 3 | |
| α-helix | 89-91 | 3 | |
| β-strand | 92-94 | 3 | 1 |
| α-helix | 103-104 | 2 | |
| α-helix | 105-109 | 5 | |
| α-helix | 111-126 | 16 | |
| 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 | 183-194 | 12 | |
| α-helix | 195-197 | 3 | |
| β-strand | 200-205 | 6 | 1 |
| α-helix | 206-216 | 11 | |
| 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 | 285-287 | 3 | |
| 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 | |
| β-strand | 343 | 1 | 3 |
| β-strand | 349-356 | 8 | 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 | 415-436 | 22 | |
Chain B: 27 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-9 | 6 | 5 |
| α-helix | 10-28 | 19 | |
| β-strand | 30 | 1 | 6 |
| β-strand | 36 | 1 | 6 |
| α-helix | 41-45 | 3 | |
| α-helix | 49-51 | 3 | |
| β-strand | 53-54 | 2 | 7 |
| β-strand | 62-63 | 2 | 7 |
| β-strand | 65-69 | 5 | 5 |
| α-helix | 73-80 | 8 | |
| 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 | 8 |
| β-strand | 177 | 1 | 8 |
| 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 | 9 |
| α-helix | 284-287 | 4 | |
| α-helix | 288-295 | 8 | |
| α-helix | 298-300 | 3 | |
| β-strand | 301 | 1 | 9 |
| α-helix | 307-309 | 3 | |
| β-strand | 312-321 | 10 | 9 |
| α-helix | 325-338 | 14 | |
| α-helix | 340-342 | 3 | |
| β-strand | 343 | 1 | 9 |
| β-strand | 351-356 | 6 | 9 |
| α-helix | 358-360 | 3 | |
| β-strand | 373-381 | 9 | 9 |
| α-helix | 382-384 | 3 | |
| α-helix | 385-399 | 15 | |
| α-helix | 406-409 | 4 | |
| α-helix | 415-437 | 23 | |
Chain C: 30 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-9 | 6 | 10 |
| α-helix | 10-28 | 19 | |
| α-helix | 48-51 | 4 | |
| β-strand | 53-55 | 3 | 11 |
| β-strand | 61-63 | 3 | 11 |
| β-strand | 65-69 | 5 | 10 |
| α-helix | 73-80 | 8 | |
| α-helix | 89-91 | 3 | |
| β-strand | 92-94 | 3 | 10 |
| 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 | 10 |
| α-helix | 144 | 1 | |
| α-helix | 145-149 | 5 | |
| α-helix | 150-161 | 12 | |
| β-strand | 165-172 | 8 | 10 |
| α-helix | 183-194 | 12 | |
| α-helix | 195-197 | 3 | |
| β-strand | 200-205 | 6 | 10 |
| α-helix | 206-216 | 11 | |
| α-helix | 224-243 | 20 | |
| α-helix | 252-259 | 8 | |
| α-helix | 268 | 1 | |
| β-strand | 269-273 | 5 | 12 |
| β-strand | 277 | 1 | 13 |
| α-helix | 278-281 | 4 | |
| α-helix | 288-294 | 7 | |
| α-helix | 298-300 | 3 | |
| β-strand | 301 | 1 | 12 |
| α-helix | 307-309 | 3 | |
| β-strand | 312-321 | 10 | 12 |
| α-helix | 325-338 | 14 | |
| β-strand | 343 | 1 | 12 |
| α-helix | 350-351 | 2 | |
| β-strand | 352-356 | 5 | 12 |
| α-helix | 359-360 | 2 | |
| β-strand | 368 | 1 | 13 |
| α-helix | 369-370 | 2 | |
| β-strand | 373-381 | 9 | 12 |
| α-helix | 382-384 | 3 | |
| α-helix | 385-399 | 15 | |
| α-helix | 405-409 | 5 | |
| α-helix | 415-436 | 22 | |
| α-helix | 438-439 | 2 | |
Chain D: 26 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-9 | 6 | 14 |
| α-helix | 10-27 | 18 | |
| β-strand | 30 | 1 | 15 |
| β-strand | 36 | 1 | 15 |
| α-helix | 41-45 | 3 | |
| α-helix | 49-51 | 3 | |
| β-strand | 53-54 | 2 | 16 |
| β-strand | 62-63 | 2 | 16 |
| β-strand | 65-69 | 5 | 14 |
| α-helix | 73-80 | 8 | |
| α-helix | 84-86 | 3 | |
| α-helix | 89-91 | 3 | |
| β-strand | 92-94 | 3 | 14 |
| α-helix | 103-108 | 6 | |
| α-helix | 110-127 | 18 | |
| β-strand | 134-140 | 7 | 14 |
| α-helix | 145-149 | 5 | |
| α-helix | 150-160 | 11 | |
| β-strand | 165-172 | 8 | 14 |
| α-helix | 183-197 | 15 | |
| β-strand | 200-205 | 6 | 14 |
| 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 | 14 |
| β-strand | 269-273 | 5 | 17 |
| α-helix | 278-281 | 4 | |
| α-helix | 288-295 | 8 | |
| α-helix | 298-300 | 3 | |
| β-strand | 301 | 1 | 17 |
| α-helix | 307-309 | 3 | |
| β-strand | 312-321 | 10 | 17 |
| α-helix | 325-338 | 14 | |
| α-helix | 340-342 | 3 | |
| β-strand | 343 | 1 | 17 |
| β-strand | 351-356 | 6 | 17 |
| α-helix | 358-360 | 3 | |
| β-strand | 373-381 | 9 | 17 |
| α-helix | 382-384 | 3 | |
| α-helix | 385-399 | 15 | |
| α-helix | 406-409 | 4 | |
| α-helix | 415-437 | 23 | |
Chain E: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 9-14 | 6 | 3 |
| β-strand | 17-25 | 9 | 3 |
| α-helix | 47-138 | 92 | |
Chain F: 14 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 18 |
| α-helix | 12-23 | 12 | |
| β-strand | 27-29 | 3 | 18 |
| α-helix | 30-31 | 2 | |
| β-strand | 39-41 | 3 | 18 |
| α-helix | 49-51 | 3 | |
| β-strand | 61-62 | 2 | 18 |
| α-helix | 69-72 | 4 | |
| α-helix | 74-83 | 10 | |
| β-strand | 97-99 | 3 | 19 |
| α-helix | 128-139 | 12 | |
| β-strand | 147-150 | 4 | 19 |
| β-strand | 161-163 | 3 | 19 |
| β-strand | 181-184 | 4 | 19 |
| β-strand | 189 | 1 | 20 |
| β-strand | 192 | 1 | 21 |
| β-strand | 197 | 1 | 21 |
| β-strand | 199-207 | 9 | 22 |
| β-strand | 213-216 | 4 | 22 |
| β-strand | 220-223 | 4 | 22 |
| α-helix | 258-260 | 3 | |
| β-strand | 261-263 | 3 | 22 |
| α-helix | 264-275 | 12 | |
| α-helix | 279 | 1 | |
| α-helix | 280-284 | 5 | |
| α-helix | 285-302 | 18 | |
| β-strand | 310-311 | 2 | 18 |
| β-strand | 313-321 | 9 | 22 |
| β-strand | 322 | 1 | 20 |
| β-strand | 327-333 | 7 | 22 |
| α-helix | 340-342 | 3 | |
| α-helix | 343-350 | 8 | |
| α-helix | 351-355 | 5 | |
| β-strand | 375-378 | 4 | 22 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Tubulin alpha-1B chain | A, C | protein | 451 | Bos taurus | P81947 (AlphaFold model) |
| Tubulin beta-2B chain | B, D | protein | 445 | Bos taurus | Q6B856 (AlphaFold model) |
| Stathmin-4 | E | protein | 189 | Rattus norvegicus | P63043 (AlphaFold model) |
| Tubulin tyrosine ligase | F | protein | 384 | Gallus gallus | A0A8V0Z8P0 (AlphaFold model) |
Sequence of entity 1 (A, C), FASTA
>9GMY_1 Tubulin alpha-1B chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY
Sequence of entity 2 (B, D), FASTA
>9GMY_2 Tubulin beta-2B chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA
Sequence of entity 3 (E), FASTA
>9GMY_3 Stathmin-4 (chains E)
MTLAAYKEKMKELPLVSLFCSCFLSDPLNKSSYKYEADTVDLNWCVISDMEVIELNKCTS
GQSFEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKR
EHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVRKN
KELKEEASR
Sequence of entity 4 (F), FASTA
>9GMY_4 Tubulin tyrosine ligase (chains F)
MYTFVVRDENSSVYAEVSRLLLATGQWKRLRKDNPRFNLMLGERNRLPFGRLGHEPGLVQ
LVNYYRGADKLCRKASLVKLIKTSPELSESCTWFPESYVIYPTNLKTPVAPAQNGIRHLI
NNTRTDEREVFLAAYNRRREGREGNVWIAKSSAGAKGEGILISSEASELLDFIDEQGQVH
VIQKYLEKPLLLEPGHRKFDIRSWVLVDHLYNIYLYREGVLRTSSEPYNSANFQDKTCHL
TNHCIQKEYSKNYGRYEEGNEMFFEEFNQYLMDALNTTLENSILLQIKHIIRSCLMCIEP
AISTKHLHYQSFQLFGFDFMVDEELKVWLIEVNGAPACAQKLYAELCQGIVDVAISSVFP
LADTGQKTSQPTSIFIKLHHHHHH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GTP | Guanosine-5'-triphosphate | C10 H16 N5 O14 P3 | 2 |
| MG | Magnesium ion | Mg | 5 |
| CA | Calcium ion | Ca | 3 |
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 2 |
| A1IM9 | (2Z,4E)-N-[(S)-[(1R,2E,5S,8E,10Z,17S)-3,11-dimethyl-7,13-bis(oxidanylidene)-6,2… | C27 H37 N O6 S | 2 |
| ACP | Phosphomethylphosphonic acid adenylate ester | C11 H18 N5 O12 P3 | 1 |
Water and common crystallization additives (CL, GOL, MES, IMD) are not listed.
Primary citation
Tubulin in complex with an oxathiane analog of zampanolide. Oliva, M.A., Diaz, J.F., Altmann, K.H. To be published.
Other PDB entries of the same protein (UniProt P81947 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6S8K 1.52 Å, Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes
- 8QL2 1.7 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
- 6ZWB 1.75 Å, Z-SBTub3 photoswitch bound to tubulin-DARPin D1 complex
- 4I4T 1.8 Å, Crystal structure of tubulin-RB3-TTL-Zampanolide complex
- 5IYZ 1.8 Å, Tubulin-MMAE complex
- 5NQU 1.8 Å, Tubulin Darpin cryo structure
- 7YZ3 1.8 Å, Molecular snapshots of drug release from tubulin: Apo state
- 8QEA 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
- 8QL3 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
- 8QL4 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
- 8QL5 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
- 8QL6 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
Browse structure collections
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