9FYD: Tubulin - cryptophycin-uD[Dab] complex
tubulin - cryptophycin-uD[Dab] complex. Determined by X-ray diffraction at 2.3 Å resolution. Released 9 Oct 2024.
- Method
- X-ray diffraction
- Resolution
- 2.3 Å
- Organisms
- Bos taurus, Rattus norvegicus, Gallus gallus
- Chains
- 6
- Atoms
- 17,954
- Mol. weight
- 265.86 kDa
- Ligands
- GTP, MG, CA, GDP
- Released
- 9 Oct 2024
Explore 9FYD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9FYD contains 133 α-helices and 97 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: 27 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-9 | 7 | 1 |
| α-helix | 10-27 | 18 | |
| β-strand | 35 | 1 | 2 |
| α-helix | 48-51 | 4 | |
| β-strand | 53-55 | 3 | 3 |
| β-strand | 60 | 1 | 2 |
| β-strand | 61-63 | 3 | 3 |
| β-strand | 65-69 | 5 | 1 |
| α-helix | 72-80 | 9 | |
| 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 | 110-112 | 3 | |
| α-helix | 115-126 | 12 | |
| β-strand | 132-140 | 9 | 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 | |
| β-strand | 269-273 | 5 | 4 |
| β-strand | 277 | 1 | 5 |
| α-helix | 288-294 | 7 | |
| α-helix | 298-300 | 3 | |
| β-strand | 301 | 1 | 4 |
| α-helix | 307-309 | 3 | |
| β-strand | 312-321 | 10 | 4 |
| α-helix | 325-338 | 14 | |
| β-strand | 343 | 1 | 4 |
| β-strand | 349-356 | 8 | 4 |
| α-helix | 359-363 | 5 | |
| β-strand | 368 | 1 | 5 |
| α-helix | 369-370 | 2 | |
| β-strand | 373-381 | 9 | 4 |
| α-helix | 382-384 | 3 | |
| α-helix | 385-400 | 16 | |
| α-helix | 405-409 | 5 | |
| α-helix | 416-436 | 21 | |
Chain B: 30 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-9 | 8 | 6 |
| α-helix | 10-27 | 18 | |
| β-strand | 30 | 1 | 7 |
| β-strand | 35 | 1 | 8 |
| β-strand | 36 | 1 | 7 |
| α-helix | 41-47 | 5 | |
| α-helix | 49-51 | 3 | |
| β-strand | 53-55 | 3 | 9 |
| α-helix | 57-59 | 3 | |
| β-strand | 60 | 1 | 8 |
| β-strand | 61-63 | 3 | 9 |
| β-strand | 65-69 | 5 | 6 |
| α-helix | 72-80 | 9 | |
| α-helix | 84-86 | 3 | |
| α-helix | 89-91 | 3 | |
| β-strand | 92-94 | 3 | 6 |
| α-helix | 103-104 | 2 | |
| α-helix | 105-109 | 5 | |
| α-helix | 110-127 | 18 | |
| β-strand | 131-140 | 10 | 6 |
| α-helix | 145-149 | 5 | |
| α-helix | 150-160 | 11 | |
| β-strand | 165-172 | 8 | 6 |
| α-helix | 173 | 1 | |
| β-strand | 174 | 1 | 10 |
| β-strand | 177 | 1 | 10 |
| α-helix | 183-197 | 15 | |
| β-strand | 200-205 | 6 | 6 |
| α-helix | 206-211 | 6 | |
| α-helix | 212-216 | 5 | |
| α-helix | 224-238 | 15 | |
| α-helix | 240-243 | 4 | |
| α-helix | 252-259 | 8 | |
| β-strand | 267-268 | 2 | 6 |
| β-strand | 269-273 | 5 | 11 |
| α-helix | 285-287 | 3 | |
| α-helix | 288-295 | 8 | |
| α-helix | 298-300 | 3 | |
| β-strand | 301 | 1 | 11 |
| α-helix | 307-309 | 3 | |
| β-strand | 312-321 | 10 | 11 |
| α-helix | 325-338 | 14 | |
| α-helix | 340-342 | 3 | |
| β-strand | 343 | 1 | 11 |
| β-strand | 351-356 | 6 | 11 |
| α-helix | 359-360 | 2 | |
| β-strand | 373-381 | 9 | 11 |
| α-helix | 382-384 | 3 | |
| α-helix | 385-399 | 15 | |
| α-helix | 406-409 | 4 | |
| α-helix | 415-436 | 22 | |
Chain C: 30 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-9 | 6 | 12 |
| α-helix | 10-28 | 19 | |
| β-strand | 35 | 1 | 13 |
| α-helix | 48-51 | 4 | |
| β-strand | 53-55 | 3 | 14 |
| β-strand | 60 | 1 | 13 |
| β-strand | 61-63 | 3 | 14 |
| β-strand | 65-69 | 5 | 12 |
| α-helix | 73-79 | 7 | |
| α-helix | 84-86 | 3 | |
| α-helix | 89-91 | 3 | |
| β-strand | 92-94 | 3 | 12 |
| α-helix | 103-104 | 2 | |
| α-helix | 105-109 | 5 | |
| α-helix | 111-127 | 17 | |
| β-strand | 134-140 | 7 | 12 |
| α-helix | 144 | 1 | |
| α-helix | 145-149 | 5 | |
| α-helix | 150-161 | 12 | |
| β-strand | 165-172 | 8 | 12 |
| α-helix | 183-194 | 12 | |
| α-helix | 195-197 | 3 | |
| β-strand | 200-205 | 6 | 12 |
| α-helix | 206-217 | 12 | |
| α-helix | 224-243 | 20 | |
| α-helix | 252-259 | 8 | |
| α-helix | 268 | 1 | |
| β-strand | 269-273 | 5 | 15 |
| β-strand | 277 | 1 | 16 |
| α-helix | 278-281 | 4 | |
| α-helix | 288-295 | 8 | |
| α-helix | 298-300 | 3 | |
| β-strand | 301 | 1 | 15 |
| α-helix | 307-309 | 3 | |
| β-strand | 312-321 | 10 | 15 |
| α-helix | 325-338 | 14 | |
| α-helix | 342 | 1 | |
| β-strand | 343 | 1 | 15 |
| α-helix | 344 | 1 | |
| β-strand | 352-356 | 5 | 15 |
| α-helix | 359-360 | 2 | |
| β-strand | 368 | 1 | 16 |
| β-strand | 373-381 | 9 | 15 |
| α-helix | 382-384 | 3 | |
| α-helix | 385-400 | 16 | |
| α-helix | 405-409 | 5 | |
| α-helix | 415-435 | 21 | |
| α-helix | 438-439 | 2 | |
Chain D: 29 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-9 | 7 | 17 |
| α-helix | 10-27 | 18 | |
| β-strand | 30 | 1 | 18 |
| β-strand | 36 | 1 | 18 |
| α-helix | 41-45 | 3 | |
| α-helix | 49-51 | 3 | |
| β-strand | 53-56 | 4 | 19 |
| α-helix | 57-59 | 3 | |
| β-strand | 60-63 | 4 | 19 |
| β-strand | 65-69 | 5 | 17 |
| α-helix | 72-79 | 8 | |
| α-helix | 84-86 | 3 | |
| α-helix | 89-91 | 3 | |
| β-strand | 92-94 | 3 | 17 |
| α-helix | 103-104 | 2 | |
| α-helix | 105-109 | 5 | |
| α-helix | 110-127 | 18 | |
| β-strand | 132-140 | 9 | 17 |
| α-helix | 145-149 | 5 | |
| α-helix | 150-160 | 11 | |
| β-strand | 165-172 | 8 | 17 |
| α-helix | 173 | 1 | |
| α-helix | 183-197 | 15 | |
| β-strand | 200-205 | 6 | 17 |
| α-helix | 206-211 | 6 | |
| α-helix | 212-216 | 5 | |
| α-helix | 224-238 | 15 | |
| α-helix | 240-243 | 4 | |
| α-helix | 252-259 | 8 | |
| β-strand | 267-268 | 2 | 17 |
| β-strand | 269-273 | 5 | 20 |
| α-helix | 288-295 | 8 | |
| α-helix | 298-300 | 3 | |
| β-strand | 301 | 1 | 20 |
| α-helix | 307-309 | 3 | |
| β-strand | 312-321 | 10 | 20 |
| α-helix | 325-338 | 14 | |
| α-helix | 340-342 | 3 | |
| β-strand | 343 | 1 | 20 |
| β-strand | 351-356 | 6 | 20 |
| α-helix | 359-360 | 2 | |
| β-strand | 373-381 | 9 | 20 |
| α-helix | 382-384 | 3 | |
| α-helix | 385-400 | 16 | |
| α-helix | 405-409 | 5 | |
| α-helix | 415-437 | 23 | |
Chain E: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-13 | 7 | 4 |
| β-strand | 17-25 | 9 | 4 |
| α-helix | 47-141 | 95 | |
Chain F: 16 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 21 |
| α-helix | 12-23 | 12 | |
| β-strand | 27-29 | 3 | 21 |
| β-strand | 39-41 | 3 | 21 |
| α-helix | 49-51 | 3 | |
| β-strand | 61-62 | 2 | 21 |
| α-helix | 68-72 | 5 | |
| α-helix | 74-83 | 10 | |
| β-strand | 97-99 | 3 | 22 |
| α-helix | 128-139 | 12 | |
| β-strand | 147-150 | 4 | 22 |
| β-strand | 161-163 | 3 | 22 |
| α-helix | 166-174 | 9 | |
| β-strand | 181-184 | 4 | 22 |
| β-strand | 189 | 1 | 23 |
| β-strand | 192 | 1 | 24 |
| β-strand | 197 | 1 | 24 |
| β-strand | 201-207 | 7 | 25 |
| β-strand | 213-216 | 4 | 25 |
| β-strand | 220-222 | 3 | 25 |
| β-strand | 227 | 1 | 24 |
| α-helix | 243-248 | 6 | |
| α-helix | 258-260 | 3 | |
| β-strand | 261-263 | 3 | 25 |
| α-helix | 264-270 | 7 | |
| α-helix | 271-275 | 5 | |
| α-helix | 279 | 1 | |
| α-helix | 280-284 | 5 | |
| α-helix | 285-302 | 18 | |
| β-strand | 310-311 | 2 | 21 |
| β-strand | 313-321 | 9 | 25 |
| β-strand | 322 | 1 | 23 |
| β-strand | 327-333 | 7 | 25 |
| α-helix | 340-342 | 3 | |
| α-helix | 343-349 | 7 | |
| α-helix | 350-355 | 6 | |
| β-strand | 375-377 | 3 | 25 |
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 | 143 | Rattus norvegicus | P63043 (AlphaFold model) |
| Tubulin tyrosine ligase | F | protein | 384 | Gallus gallus | A0A8V0Z8P0 (AlphaFold model) |
Sequence of entity 1 (A, C), FASTA
>9FYD_1 Tubulin alpha-1B chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY
Sequence of entity 2 (B, D), FASTA
>9FYD_2 Tubulin beta-2B chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA
Sequence of entity 3 (E), FASTA
>9FYD_3 Stathmin-4 (chains E)
MADMEVIELNKCTSGQSFEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRK
YQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLER
LQEKDKHAEEVRKNKELKEEASR
Sequence of entity 4 (F), FASTA
>9FYD_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 | 4 |
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 2 |
| A1IHR | cryptophycin-uD[Dab] | C34 H43 Cl N4 O7 | 2 |
| ACP | Phosphomethylphosphonic acid adenylate ester | C11 H18 N5 O12 P3 | 1 |
Water and common crystallization additives (MES) are not listed.
Primary citation
Highly Cytotoxic Cryptophycin Derivatives with Modification in Unit D for Conjugation. Dessin, C., Schachtsiek, T., Voss, J. et al. Angew Chem Int Ed Engl (2024) 63:e202416210-e202416210. DOI 10.1002/anie.202416210 · PubMed
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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