7TTF: Tubulin-RB3_SLD

Tubulin-RB3_SLD in complex with compound 12k. Determined by X-ray diffraction at 2.1 Å resolution. Released 12 Apr 2023.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Sus scrofa, Rattus norvegicus
Chains: 5
Atoms: 14,849
Mol. weight: 215.16 kDa
Ligands: MG, JV9, GDP, GTP
Released: 12 Apr 2023

Explore 7TTF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7TTF 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	105-110	6
α-helix	111-127	17
β-strand	134-140	7	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	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	385-400	16
α-helix	405-409	5
α-helix	416-436	21

Chain B: 27 helices, 19 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	41-43	3
α-helix	47-49	3
β-strand	51-53	3	8
β-strand	58	1	7
β-strand	59-61	3	8
β-strand	63-67	5	5
α-helix	71-77	7
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	9
α-helix	286-291	6
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	357-358	2
β-strand	364-371	8	9
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	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	183-195	13
β-strand	200-205	6	10
α-helix	206-217	12
α-helix	224-243	20
β-strand	248	1	10
α-helix	252-259	8
β-strand	269-273	5	10
β-strand	277	1	12
α-helix	288-295	8
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
α-helix	342	1
β-strand	343	1	10
α-helix	344	1
β-strand	351-356	6	10
α-helix	359-360	2
β-strand	368	1	12
α-helix	369-370	2
β-strand	373-381	9	10
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-410	6
α-helix	415-435	21

Chain D: 26 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	13
α-helix	10-28	19
β-strand	30	1	14
β-strand	35	1	15
β-strand	36	1	14
α-helix	41-43	3
α-helix	47-49	3
β-strand	51-53	3	16
β-strand	58	1	15
β-strand	59-61	3	16
β-strand	63-67	5	13
α-helix	71-78	8
α-helix	82-84	3
α-helix	87-89	3
β-strand	90-92	3	13
α-helix	101-106	6
α-helix	108-125	18
β-strand	130-138	9	13
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-170	8	13
α-helix	181-195	15
β-strand	198-203	6	13
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	13
β-strand	267-271	5	17
α-helix	286-293	8
α-helix	296-298	3
β-strand	299	1	17
α-helix	305-307	3
β-strand	310-318	9	17
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	17
β-strand	349-354	6	17
α-helix	357-358	2
β-strand	364-371	8	17
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	8-14	7	3
β-strand	17-25	9	3
α-helix	47-139	93

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	P02554 (AlphaFold model)
Stathmin-4	E	protein	143	Rattus norvegicus	P63043 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7TTF_1 Tubulin alpha-1B chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVD

Sequence of entity 2 (B, D), FASTA

>7TTF_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQ

Sequence of entity 3 (E), FASTA

>7TTF_3 Stathmin-4 (chains E)
MADMEVIELNKATSGQSWEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRK
YQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLER
LQEKDKHAEEVRKNKELKEEASR

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
JV9	7-methoxy-4-[2-(methylamino)-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl]-3,4-di…	C17 H19 N5 O2	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	3

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

Primary citation

Design, Synthesis, and Biological Evaluation of Pyrimidine Dihydroquinoxalinone Derivatives as Tubulin Colchicine Site-Binding Agents That Displayed Potent Anticancer Activity Both In Vitro and In Vivo. Pochampally, S., Hartman, K.L., Wang, R. et al. Acs Pharmacol Transl Sci (2023) 6:526-545. DOI 10.1021/acsptsci.2c00108 · 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
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
5XP3 2.3 Å, Crystal structure of apo T2R-TTL

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