9MLF: Tubulin-RB3_SLD

Tubulin-RB3_SLD in complex with compound qw-4-183-llb. Determined by X-ray diffraction at 2.4 Å resolution. Released 12 Nov 2025.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Sus scrofa, Rattus norvegicus
Chains: 5
Atoms: 14,678
Mol. weight: 214.52 kDa
Ligands: GTP, MG, A1BMG, GDP
Released: 12 Nov 2025

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

Secondary structure: helices and β-sheets

9MLF contains 106 α-helices and 73 β-strands across 5 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, 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	65-68	4	1
α-helix	72-80	9
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-93	2	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	110-126	17
β-strand	134-140	7	1
α-helix	144-160	17
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	206-217	12
α-helix	224-243	20
α-helix	252-259	8
β-strand	269-273	5	3
β-strand	277	1	4
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	359-360	2
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	415-435	21

Chain B: 26 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	5
α-helix	10-28	19
β-strand	30	1	6
β-strand	35	1	7
β-strand	36	1	6
α-helix	47-49	3
β-strand	51-54	4	7
β-strand	58-61	4	7
β-strand	63-67	5	5
α-helix	70-77	8
α-helix	82-84	3
α-helix	87-89	3
β-strand	90-92	3	5
α-helix	101-105	5
α-helix	107-125	19
β-strand	130-138	9	5
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-170	8	5
α-helix	171	1
α-helix	173-175	3
α-helix	181-195	15
β-strand	198-203	6	5
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-241	20
α-helix	250-257	8
β-strand	265-266	2	5
β-strand	267-271	5	8
α-helix	286-293	8
α-helix	296-298	3
β-strand	299	1	8
α-helix	305-307	3
β-strand	310-318	9	8
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	8
β-strand	349-354	6	8
α-helix	357-358	2
β-strand	364-371	8	8
α-helix	372-374	3
α-helix	375-389	15
α-helix	396-399	4
α-helix	405-427	23

Chain C: 27 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	9
α-helix	10-28	19
α-helix	48-51	4
β-strand	53-55	3	10
β-strand	61-63	3	10
β-strand	65-69	5	9
α-helix	73-79	7
α-helix	89-91	3
β-strand	92-94	3	9
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-126	12
β-strand	134-140	7	9
α-helix	144	1
α-helix	145-149	5
α-helix	150-161	12
β-strand	165-172	8	9
α-helix	175-177	3
α-helix	183-195	13
β-strand	200-205	6	9
α-helix	206-215	10
α-helix	224-243	20
β-strand	248	1	9
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	9
β-strand	277	1	11
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	9
α-helix	307-309	3
β-strand	312-321	10	9
α-helix	325-337	13
β-strand	343	1	9
β-strand	351-356	6	9
α-helix	359-361	3
β-strand	368	1	11
α-helix	369-370	2
β-strand	373-381	9	9
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	415-435	21

Chain D: 27 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	12
α-helix	10-28	19
β-strand	30	1	13
β-strand	35	1	14
β-strand	36	1	13
α-helix	42-45	4
α-helix	47-49	3
β-strand	51-54	4	14
β-strand	58-61	4	14
β-strand	63-67	5	12
α-helix	71-78	8
α-helix	82-84	3
α-helix	87-89	3
β-strand	90-92	3	12
α-helix	101-105	5
α-helix	110-125	16
β-strand	130-138	9	12
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-170	8	12
α-helix	171	1
β-strand	172	1	15
β-strand	175	1	15
α-helix	181-195	15
β-strand	198-203	6	12
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-241	20
α-helix	250-257	8
β-strand	265-266	2	12
β-strand	267-271	5	16
α-helix	283-285	3
α-helix	286-293	8
α-helix	296-298	3
β-strand	299	1	16
α-helix	305-307	3
β-strand	310-319	10	16
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	16
β-strand	349-354	6	16
α-helix	357-358	2
β-strand	363-371	9	16
α-helix	372-374	3
α-helix	375-389	15
α-helix	396-399	4
α-helix	405-427	23

Chain E: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	3
β-strand	17-25	9	3
α-helix	47-138	92

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A, C	protein	438	Sus scrofa	Q2XVP4 (AlphaFold model)
Tubulin beta chain	B, D	protein	433	Sus scrofa	A0A8D1UIR5 (AlphaFold model)
Stathmin-4	E	protein	143	Rattus norvegicus	P63043 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9MLF_1 Tubulin alpha-1B chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVD

Sequence of entity 2 (B, D), FASTA

>9MLF_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQ

Sequence of entity 3 (E), FASTA

>9MLF_3 Stathmin-4 (chains E)
MADMEVIELNKATSGQSWEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRK
YQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLER
LQEKDKHAEEVRKNKELKEEASR

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
MG	Magnesium ion	Mg	1
A1BMG	[(4M)-4-(1H-indol-4-yl)-1H-imidazol-2-yl](3,4,5-trimethoxyphenyl)methanone	C21 H19 N3 O4	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Design and synthesis of novel 4-aryl-2-benzoyl-imidazoles as colchicine binding site inhibitors. Albadari, N., Xie, Y., Wang, Q. et al. Eur J Med Chem (2025) 298:118021-118021. DOI 10.1016/j.ejmech.2025.118021 · 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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