6TDE: Tubulin-inhibitor complex

Tubulin-inhibitor complex. Determined by X-ray diffraction at 2.29 Å resolution. Released 2 Sept 2020.

Method: X-ray diffraction
Resolution: 2.29 Å
Organisms: Ovis aries, Rattus norvegicus
Chains: 5
Atoms: 15,022
Mol. weight: 220.79 kDa
Ligands: N3Z, GDP, MG, GTP
Released: 2 Sept 2020

Explore 6TDE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6TDE contains 117 α-helices and 75 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: 29 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-28	19
α-helix	47-51	5
β-strand	53-55	3	2
β-strand	61-63	3	2
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	111-126	16
β-strand	134-140	7	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	206-215	10
α-helix	224-243	20
α-helix	253-259	7
α-helix	268	1
β-strand	269-273	5	3
β-strand	277	1	4
α-helix	284-287	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
α-helix	342	1
β-strand	343	1	3
α-helix	344	1
β-strand	349-356	8	3
α-helix	359-361	3
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: 29 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	5
α-helix	10-27	18
β-strand	30	1	6
β-strand	36	1	6
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-56	4	7
α-helix	57-59	3
β-strand	60-63	4	7
β-strand	65-69	5	5
α-helix	72-80	9
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	5
α-helix	103-104	2
α-helix	105-109	5
α-helix	110-127	18
β-strand	134-140	7	5
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	5
α-helix	173	1
β-strand	174	1	8
β-strand	177	1	8
α-helix	183-197	15
β-strand	200-205	6	5
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	5
β-strand	269-273	5	9
α-helix	288-293	6
α-helix	298-300	3
β-strand	301	1	9
α-helix	307-309	3
β-strand	312-320	9	9
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	9
β-strand	351-356	6	9
α-helix	359-360	2
β-strand	374-381	8	9
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-437	23

Chain C: 30 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	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	111-113	3
α-helix	115-126	12
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	183-194	12
α-helix	195-197	3
β-strand	200-205	6	10
α-helix	206-215	10
α-helix	224-243	20
β-strand	248	1	13
α-helix	252-259	8
β-strand	262	1	14
β-strand	265	1	14
α-helix	268	1
β-strand	269-273	5	13
β-strand	277	1	15
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	13
α-helix	307-309	3
β-strand	312-321	10	13
α-helix	325-336	12
α-helix	342	1
β-strand	343	1	13
α-helix	344	1
β-strand	351-356	6	13
α-helix	359-361	3
β-strand	368	1	15
α-helix	369-370	2
β-strand	373-381	9	13
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	415-436	22
α-helix	438-439	2

Chain D: 28 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	16
α-helix	10-27	18
β-strand	30	1	17
β-strand	36	1	17
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-56	4	18
α-helix	57-59	3
β-strand	60-63	4	18
β-strand	65-69	5	16
α-helix	72-80	9
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	16
α-helix	103-107	5
α-helix	110-127	18
β-strand	134-140	7	16
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	16
α-helix	183-197	15
β-strand	200-205	6	16
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	16
β-strand	269-273	5	19
α-helix	288-293	6
α-helix	294-296	3
α-helix	298-300	3
β-strand	301	1	19
α-helix	307-309	3
β-strand	312-321	10	19
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	19
β-strand	351-356	6	19
α-helix	359-360	2
β-strand	373-381	9	19
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-437	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	47-140	94

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha chain	A, C	protein	451	Ovis aries	D0VWZ0 (AlphaFold model)
Tubulin beta chain	B, D	protein	445	Ovis aries	D0VWY9 (AlphaFold model)
Stathmin-4	E	protein	143	Rattus norvegicus	P63043 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6TDE_1 Tubulin alpha chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D), FASTA

>6TDE_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (E), FASTA

>6TDE_3 Stathmin-4 (chains E)
XADMEVIELNKATSGQSWEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRK
YQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLER
LQEKDKHAEEVRKNKELKEEASR

Ligands and cofactors

ID	Name	Formula	Copies
N3Z	~{N}-[(10~{S})-3,4,5-trimethoxy-16-methylidene-14-oxatetracyclo[9.7.0.0^{2,7}.0…	C23 H25 N O5	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
MG	Magnesium ion	Mg	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

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

Primary citation

Discovery of dihydrofuranoallocolchicinoids - Highly potent antimitotic agents with low acute toxicity. Shchegravina, E.S., Svirshchevskaya, E.V., Combes, S. et al. Eur J Med Chem (2020) 207:112724-112724. DOI 10.1016/j.ejmech.2020.112724 · PubMed

Other PDB entries of the same protein (UniProt D0VWZ0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EYP 1.9 Å, Tubulin-darpin complex
3RYC 2.1 Å, Tubulin: RB3 stathmin-like domain complex
9F07 2.21 Å, Tubulin:stathmin:darpin:tau MTBR3 complex
4DRX 2.22 Å, GTP-Tubulin in complex with a DARPIN
3RYI 2.4 Å, GDP-Tubulin: rb3 stathmin-like domain complex
5KX5 2.5 Å, Crystal structure of tubulin-stathmin-TTL-Compound 11 complex
3RYF 2.52 Å, GTP-Tubulin: RB3 Stathmin-like domain complex
4F6R 2.64 Å, Tubulin:Stathmin-like domain complex
6GVN 2.69 Å, Tubulin:TM-3 DARPin complex
3UT5 2.73 Å, Tubulin-Colchicine-Ustiloxin: Stathmin-like domain complex
6H9B 2.75 Å, 1,1-Diheterocyclic Ethylenes Derived from Quinaldine and Carbazole as New Tubulin…
3RYH 2.8 Å, GMPCPP-Tubulin: RB3 Stathmin-like domain complex

Browse structure collections

About this viewer

MolViewer shows 6TDE directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.