9KBL: T2R-TTL-IKP104
Crystal structure of T2R-TTL-IKP104. Determined by X-ray diffraction at 3.14 Å resolution. Released 5 Nov 2025.
- Method
- X-ray diffraction
- Resolution
- 3.14 Å
- Organisms
- Sus scrofa, Rattus norvegicus, Gallus gallus
- Chains
- 6
- Atoms
- 17,610
- Mol. weight
- 261.98 kDa
- Ligands
- GTP, MG, GDP, W4Q
- Released
- 5 Nov 2025
Explore 9KBL in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9KBL contains 121 α-helices and 96 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: 25 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-9 | 7 | 1 |
| α-helix | 10-28 | 19 | |
| 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 | 89-91 | 3 | |
| β-strand | 92-94 | 3 | 1 |
| α-helix | 103-104 | 2 | |
| α-helix | 105-109 | 5 | |
| α-helix | 110-127 | 18 | |
| β-strand | 132-140 | 9 | 1 |
| α-helix | 144-160 | 17 | |
| β-strand | 165-172 | 8 | 1 |
| α-helix | 183-194 | 12 | |
| α-helix | 195-197 | 3 | |
| β-strand | 200-205 | 6 | 1 |
| α-helix | 206-217 | 12 | |
| α-helix | 224-243 | 20 | |
| α-helix | 252-259 | 8 | |
| α-helix | 268 | 1 | |
| β-strand | 269-273 | 5 | 4 |
| β-strand | 277 | 1 | 5 |
| α-helix | 284-287 | 4 | |
| 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 | 359-361 | 3 | |
| β-strand | 368 | 1 | 5 |
| α-helix | 369-370 | 2 | |
| β-strand | 373-381 | 9 | 4 |
| α-helix | 382-384 | 3 | |
| α-helix | 385-399 | 15 | |
| α-helix | 405-409 | 5 | |
| α-helix | 415-436 | 22 | |
Chain B: 27 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-9 | 7 | 6 |
| α-helix | 10-27 | 18 | |
| β-strand | 30 | 1 | 7 |
| β-strand | 35 | 1 | 8 |
| β-strand | 36 | 1 | 7 |
| α-helix | 42-45 | 4 | |
| α-helix | 47-49 | 3 | |
| β-strand | 51-54 | 4 | 8 |
| β-strand | 58-61 | 4 | 8 |
| β-strand | 63-67 | 5 | 6 |
| α-helix | 71-78 | 8 | |
| α-helix | 87-89 | 3 | |
| β-strand | 90-92 | 3 | 6 |
| α-helix | 101-102 | 2 | |
| α-helix | 103-107 | 5 | |
| α-helix | 110-124 | 15 | |
| β-strand | 130-138 | 9 | 6 |
| α-helix | 143-147 | 5 | |
| α-helix | 148-158 | 11 | |
| β-strand | 163-170 | 8 | 6 |
| α-helix | 171-172 | 2 | |
| α-helix | 181-195 | 15 | |
| β-strand | 198-203 | 6 | 6 |
| α-helix | 204-209 | 6 | |
| α-helix | 210-214 | 5 | |
| α-helix | 222-236 | 15 | |
| α-helix | 238-241 | 4 | |
| α-helix | 250-257 | 8 | |
| β-strand | 265-266 | 2 | 6 |
| β-strand | 267-271 | 5 | 9 |
| α-helix | 286-294 | 9 | |
| α-helix | 296-298 | 3 | |
| β-strand | 299 | 1 | 9 |
| α-helix | 305-307 | 3 | |
| β-strand | 310-318 | 9 | 9 |
| α-helix | 323-336 | 14 | |
| α-helix | 338-340 | 3 | |
| β-strand | 341 | 1 | 9 |
| β-strand | 349-354 | 6 | 9 |
| α-helix | 356-358 | 3 | |
| β-strand | 372-379 | 8 | 9 |
| α-helix | 380-382 | 3 | |
| α-helix | 383-397 | 15 | |
| α-helix | 404-407 | 4 | |
| α-helix | 413-434 | 22 | |
Chain C: 25 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-9 | 7 | 10 |
| α-helix | 10-28 | 19 | |
| β-strand | 35 | 1 | 11 |
| α-helix | 48-51 | 4 | |
| β-strand | 53-55 | 3 | 12 |
| β-strand | 60 | 1 | 11 |
| β-strand | 61-63 | 3 | 12 |
| 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 | 111-127 | 17 | |
| β-strand | 132-138 | 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 | |
| β-strand | 200-205 | 6 | 10 |
| α-helix | 206-217 | 12 | |
| α-helix | 224-243 | 20 | |
| α-helix | 252-259 | 8 | |
| β-strand | 262 | 1 | 13 |
| β-strand | 265 | 1 | 13 |
| β-strand | 269-273 | 5 | 10 |
| β-strand | 277 | 1 | 14 |
| α-helix | 278-281 | 4 | |
| α-helix | 288-294 | 7 | |
| α-helix | 298-300 | 3 | |
| β-strand | 301 | 1 | 10 |
| α-helix | 307-309 | 3 | |
| β-strand | 312-321 | 10 | 10 |
| α-helix | 325-335 | 11 | |
| β-strand | 343 | 1 | 10 |
| β-strand | 351-356 | 6 | 10 |
| α-helix | 359-360 | 2 | |
| β-strand | 368 | 1 | 14 |
| β-strand | 373-381 | 9 | 10 |
| α-helix | 382-384 | 3 | |
| α-helix | 385-399 | 15 | |
| α-helix | 405-409 | 5 | |
| α-helix | 415-434 | 20 | |
| α-helix | 438-439 | 2 | |
Chain D: 26 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-9 | 8 | 15 |
| α-helix | 10-27 | 18 | |
| β-strand | 30 | 1 | 16 |
| β-strand | 35 | 1 | 17 |
| β-strand | 36 | 1 | 16 |
| α-helix | 41-43 | 3 | |
| α-helix | 47-49 | 3 | |
| β-strand | 51-54 | 4 | 17 |
| β-strand | 58-61 | 4 | 17 |
| β-strand | 63-67 | 5 | 15 |
| α-helix | 70-78 | 9 | |
| α-helix | 87-89 | 3 | |
| β-strand | 90-92 | 3 | 15 |
| α-helix | 101-102 | 2 | |
| α-helix | 103-107 | 5 | |
| α-helix | 108-125 | 18 | |
| β-strand | 129-138 | 10 | 15 |
| α-helix | 143-147 | 5 | |
| α-helix | 148-158 | 11 | |
| β-strand | 163-170 | 8 | 15 |
| α-helix | 181-195 | 15 | |
| β-strand | 198-203 | 6 | 15 |
| α-helix | 204-209 | 6 | |
| α-helix | 210-214 | 5 | |
| α-helix | 222-236 | 15 | |
| α-helix | 238-241 | 4 | |
| α-helix | 250-257 | 8 | |
| β-strand | 265-266 | 2 | 15 |
| β-strand | 267-271 | 5 | 18 |
| α-helix | 286-293 | 8 | |
| α-helix | 296-298 | 3 | |
| β-strand | 299 | 1 | 18 |
| α-helix | 305-307 | 3 | |
| β-strand | 310-319 | 10 | 18 |
| α-helix | 323-336 | 14 | |
| α-helix | 338-340 | 3 | |
| β-strand | 341 | 1 | 18 |
| β-strand | 349-354 | 6 | 18 |
| α-helix | 357-358 | 2 | |
| β-strand | 371-379 | 9 | 18 |
| α-helix | 380-382 | 3 | |
| α-helix | 383-397 | 15 | |
| α-helix | 404-407 | 4 | |
| α-helix | 413-434 | 22 | |
Chain E: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-13 | 7 | 4 |
| β-strand | 17-25 | 9 | 4 |
| α-helix | 47-121 | 75 | |
| α-helix | 125-128 | 4 | |
| α-helix | 130-138 | 9 | |
Chain F: 15 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 19 |
| α-helix | 12-23 | 12 | |
| β-strand | 27-29 | 3 | 19 |
| β-strand | 39-41 | 3 | 19 |
| α-helix | 49-51 | 3 | |
| β-strand | 61-62 | 2 | 19 |
| α-helix | 68-70 | 3 | |
| α-helix | 74-82 | 9 | |
| β-strand | 97-100 | 4 | 20 |
| α-helix | 128-140 | 13 | |
| β-strand | 147-150 | 4 | 20 |
| β-strand | 161-163 | 3 | 20 |
| α-helix | 166-174 | 9 | |
| β-strand | 180-184 | 5 | 20 |
| β-strand | 189 | 1 | 21 |
| β-strand | 192 | 1 | 22 |
| β-strand | 197 | 1 | 22 |
| β-strand | 199-207 | 9 | 23 |
| β-strand | 213-216 | 4 | 23 |
| β-strand | 220-223 | 4 | 23 |
| α-helix | 243-248 | 6 | |
| α-helix | 258-260 | 3 | |
| β-strand | 261-263 | 3 | 23 |
| α-helix | 264-275 | 12 | |
| α-helix | 279 | 1 | |
| α-helix | 280-284 | 5 | |
| α-helix | 285-302 | 18 | |
| β-strand | 310-311 | 2 | 19 |
| β-strand | 313-321 | 9 | 23 |
| β-strand | 322 | 1 | 21 |
| β-strand | 327-333 | 7 | 23 |
| α-helix | 340-342 | 3 | |
| α-helix | 343-350 | 8 | |
| α-helix | 351-355 | 5 | |
| β-strand | 375-377 | 3 | 23 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Tubulin alpha-1B chain | A, C | protein | 451 | Sus scrofa | Q2XVP4 (AlphaFold model) |
| Tubulin beta chain | B, D | protein | 431 | Sus scrofa | A0A8D0VN39 (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
>9KBL_1 Tubulin alpha-1B chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY
Sequence of entity 2 (B, D), FASTA
>9KBL_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAD
Sequence of entity 3 (E), FASTA
>9KBL_3 Stathmin-4 (chains E)
MADMEVIELNKCTSGQSFEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRK
YQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLER
LQEKDKHAEEVRKNKELKEEASR
Sequence of entity 4 (F), FASTA
>9KBL_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 | 3 |
| MG | Magnesium ion | Mg | 5 |
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 1 |
| W4Q | 1-(2-chloranyl-3,5-dimethoxy-phenyl)-2-(4-fluorophenyl)-3-methyl-6-phenyl-pyrid… | C26 H21 Cl F N O3 | 1 |
| CA | Calcium ion | Ca | 7 |
| ACP | Phosphomethylphosphonic acid adenylate ester | C11 H18 N5 O12 P3 | 1 |
Water and common crystallization additives (MES) are not listed.
Primary citation
Crystal structure of T2R-TTL-IKP104. Yan, W., Yang, J. To be published.
Other PDB entries of the same protein (UniProt Q2XVP4 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9U6A 1.92 Å, Tubulin-DARPin D1 in complex with a flavone
- 5EZY 2.05 Å, Crystal structure of T2R-TTL-taccalonolide AJ complex
- 5YL2 2.09 Å, Crystal structure of T2R-TTL-Y28 complex
- 7TTF 2.1 Å, Tubulin-RB3_SLD in complex with compound 12k
- 5XKG 2.2 Å, Crystal structure of T2R-TTL-CH1 complex
- 7L05 2.21 Å, Complex of novel maytansinoid M24 bound to T2R-TTL (two tubulin alpha/beta heterodimers,…
- 9M1M 2.21 Å, Cryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
- 5JQG 2.24 Å, An apo tubulin-RB-TTL complex structure used for side-by-side comparison
- 9M1N 2.24 Å, Cryo-EM structure of the TBC-DC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
- 5XKH 2.25 Å, Crystal structure of T2R-TTL-CF1 complex
- 7TTD 2.27 Å, Tubulin-RB3_SLD in complex with compound 12e
- 5JCB 2.3 Å, Microtubule depolymerizing agent podophyllotoxin derivative YJTSF1
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