9U6D: Tubulin-RB3-TTL

Crystal structure of tubulin-RB3-TTL in complex with X8. Determined by X-ray diffraction at 2.54 Å resolution. Released 25 Mar 2026.

Method: X-ray diffraction
Resolution: 2.54 Å
Organisms: Sus scrofa, Rattus norvegicus, Gallus gallus
Chains: 6
Atoms: 17,679
Mol. weight: 267.07 kDa
Ligands: GDP, CA, MG, GTP
Released: 25 Mar 2026

Explore 9U6D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9U6D contains 131 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: 30 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	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	115-126	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	175-177	3
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	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
α-helix	342	1
β-strand	343	1	4
α-helix	344	1
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, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	6
α-helix	10-27	18
β-strand	30	1	7
β-strand	36	1	7
α-helix	41-45	3
α-helix	49-51	3
β-strand	53-56	4	8
β-strand	60-63	4	8
β-strand	65-69	5	6
α-helix	72-79	8
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	6
α-helix	103-107	5
α-helix	110-127	18
β-strand	132-140	9	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	9
β-strand	177	1	9
α-helix	183-197	15
β-strand	200-205	6	6
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	6
β-strand	269-273	5	10
α-helix	284-287	4
α-helix	288-296	9
α-helix	298-300	3
β-strand	301	1	10
α-helix	307-309	3
β-strand	312-320	9	10
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	10
β-strand	351-356	6	10
α-helix	359-360	2
β-strand	366-373	8	10
α-helix	374-376	3
α-helix	377-391	15
α-helix	398-401	4
α-helix	407-429	23

Chain C: 32 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	11
α-helix	10-28	19
β-strand	35	1	12
α-helix	48-51	4
β-strand	53-55	3	13
β-strand	60	1	12
β-strand	61-63	3	13
β-strand	65-69	5	11
α-helix	73-80	8
α-helix	89-91	3
β-strand	92-94	3	11
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-126	12
β-strand	132-140	9	11
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	11
α-helix	175-177	3
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	11
α-helix	206-216	11
α-helix	224-243	20
α-helix	249-251	3
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	14
α-helix	278-281	4
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	14
α-helix	307-309	3
β-strand	312-321	10	14
α-helix	325-338	14
α-helix	342	1
β-strand	343	1	14
α-helix	344	1
β-strand	352-356	5	14
α-helix	359-361	3
α-helix	369-370	2
β-strand	373-381	9	14
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	415-436	22

Chain D: 25 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	15
α-helix	10-27	18
β-strand	30	1	16
β-strand	36	1	16
α-helix	41-45	3
α-helix	49-51	3
β-strand	53-56	4	17
β-strand	60-63	4	17
β-strand	65-69	5	15
α-helix	72-80	9
α-helix	89-91	3
β-strand	92-94	3	15
α-helix	103-104	2
α-helix	105-109	5
α-helix	110-127	18
β-strand	132-140	9	15
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	15
α-helix	183-197	15
β-strand	200-205	6	15
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	15
β-strand	269-273	5	18
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	18
α-helix	307-309	3
β-strand	312-320	9	18
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	18
β-strand	351-356	6	18
α-helix	359-360	2
β-strand	366-373	8	18
α-helix	374-376	3
α-helix	377-391	15
α-helix	398-401	4
α-helix	407-429	23

Chain E: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	4
β-strand	17-25	9	4
α-helix	47-141	95

Chain F: 16 helices, 18 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	74-83	10
β-strand	97-99	3	20
α-helix	128-135	8
β-strand	147-150	4	20
β-strand	156-159	4	21
β-strand	161-163	3	20
α-helix	166-174	9
β-strand	181-184	4	20
α-helix	185	1
β-strand	189	1	22
β-strand	201-207	7	22
β-strand	213-216	4	22
β-strand	220-221	2	22
α-helix	258-260	3
β-strand	262-263	2	22
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	19
β-strand	313-322	10	22
β-strand	326-333	8	22
α-helix	340-342	3
α-helix	343-350	8
α-helix	351-355	5
β-strand	375-377	3	22

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	P02554 (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

>9U6D_1 Tubulin alpha-1B chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D), FASTA

>9U6D_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAD

Sequence of entity 3 (E), FASTA

>9U6D_3 Stathmin-4 (chains E)
MTLAAYKEKMKELPLVSLFCSCFLSDPLNKSSYKYEADTVDLNWCVISDMEVIELNKCTS
GQSFEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKR
EHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVRKN
KELKEEASR

Sequence of entity 4 (F), FASTA

>9U6D_4 Tubulin--tyrosine ligase (chains F)
MYTFVVRDENSSVYAEVSRLLLATGQWKRLRKDNPRFNLMLGERNRLPFGRLGHEPGLVQ
LVNYYRGADKLCRKASLVKLIKTSPELSESCTWFPESYVIYPTNLKTPVAPAQNGIRHLI
NNTRTDEREVFLAAYNRRREGREGNVWIAKSSAGAKGEGILISSEASELLDFIDEQGQVH
VIQKYLEKPLLLEPGHRKFDIRSWVLVDHLYNIYLYREGVLRTSSEPYNSANFQDKTCHL
TNHCIQKEYSKNYGRYEEGNEMFFEEFNQYLMDALNTTLENSILLQIKHIIRSCLMCIEP
AISTKHLHYQSFQLFGFDFMVDEELKVWLIEVNGAPACAQKLYAELCQGIVDVAISSVFP
LADTGQKTSQPTSIFIKLHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
CA	Calcium ion	Ca	6
MG	Magnesium ion	Mg	5
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
A1L8Z	2-[2-fluoranyl-4-[4-[2-[4-[(1~{R},2~{S})-2-fluoranylcyclopropyl]carbonylpiperaz…	C31 H33 F2 N3 O3	2

Water and common crystallization additives (MES) are not listed.

Primary citation

Structure-based design and synthesis of KX-01 analogs as potent antitumor agents targeting the tubulin colchicine binding site. Zhang, C., Wang, Y., Gao, C. et al. Eur J Med Chem (2026) 312:118849-118849. DOI 10.1016/j.ejmech.2026.118849 · PubMed

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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