5KX5: Tubulin-stathmin-TTL-Compound 11 complex

Crystal structure of tubulin-stathmin-TTL-Compound 11 complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 28 Dec 2016.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Ovis aries, Rattus norvegicus, Gallus gallus
Chains: 6
Atoms: 17,802
Mol. weight: 265.7 kDa
Ligands: 6YK, GDP, CA, MG
Released: 28 Dec 2016

Explore 5KX5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KX5 contains 124 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: 26 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10-27	18
α-helix	48-51	4
β-strand	53-55	3	2
β-strand	61-63	3	2
β-strand	65-69	5	1
α-helix	72-75	4
α-helix	89-91	3
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-111	7
α-helix	112	1
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	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
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	359-361	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	406-409	4
α-helix	415-436	22

Chain B: 26 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	5
α-helix	10-27	18
β-strand	30	1	6
β-strand	35	1	7
β-strand	36	1	6
α-helix	41-45	3
α-helix	49-51	3
β-strand	53-56	4	7
β-strand	60-63	4	7
β-strand	65-69	5	5
α-helix	73-80	8
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	132-140	9	5
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	5
α-helix	173	1
α-helix	183-197	15
β-strand	200-205	6	5
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	5
β-strand	269-273	5	8
α-helix	285-287	3
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	8
α-helix	307-309	3
β-strand	312-321	10	8
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	8
β-strand	351-356	6	8
β-strand	373-381	9	8
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-436	22

Chain C: 30 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	9
α-helix	10-28	19
β-strand	35	1	10
α-helix	48-51	4
β-strand	53-55	3	11
β-strand	60	1	10
β-strand	61-63	3	11
β-strand	65-69	5	9
α-helix	72-80	9
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	115-127	13
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	183-195	13
β-strand	200-205	6	9
α-helix	206-215	10
α-helix	224-243	20
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	12
β-strand	277	1	13
α-helix	278-281	4
α-helix	285-287	3
α-helix	288-293	6
α-helix	294-296	3
α-helix	298-300	3
β-strand	301	1	12
α-helix	307-309	3
β-strand	312-321	10	12
α-helix	325-337	13
β-strand	343	1	12
β-strand	352-356	5	12
α-helix	359-361	3
β-strand	368	1	13
α-helix	369-370	2
β-strand	373-381	9	12
α-helix	382-384	3
α-helix	385-400	16
α-helix	406-409	4
α-helix	415-435	21
α-helix	438-439	2

Chain D: 27 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	14
α-helix	10-28	19
β-strand	30	1	15
β-strand	36	1	15
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-56	4	16
β-strand	60-63	4	16
β-strand	65-69	5	14
α-helix	73-80	8
α-helix	89-91	3
β-strand	92-94	3	14
α-helix	103-104	2
α-helix	105-109	5
α-helix	110-127	18
β-strand	132-140	9	14
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	14
α-helix	173	1
α-helix	183-197	15
β-strand	200-205	6	14
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	14
β-strand	269-273	5	17
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	17
α-helix	307-309	3
β-strand	312-321	10	17
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	17
β-strand	351-356	6	17
α-helix	359-360	2
β-strand	373-381	9	17
α-helix	382-384	3
α-helix	385-401	17
α-helix	406-409	4
α-helix	416-437	22

Chain E: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	3
β-strand	17-25	9	3
α-helix	47-138	92

Chain F: 14 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	18
α-helix	12-22	11
β-strand	27-29	3	18
α-helix	30-31	2
β-strand	39-41	3	18
β-strand	61-62	2	18
α-helix	69-72	4
α-helix	74-83	10
β-strand	97-100	4	19
α-helix	128-139	12
β-strand	147-151	5	19
β-strand	161-163	3	19
α-helix	166-173	8
β-strand	180-184	5	19
β-strand	189	1	20
β-strand	192	1	21
β-strand	197	1	21
β-strand	201-207	7	22
β-strand	213-222	10	22
α-helix	227-228	2
α-helix	243-246	4
β-strand	261-263	3	22
α-helix	264-275	12
α-helix	279	1
α-helix	280-284	5
α-helix	285-302	18
β-strand	310-311	2	18
β-strand	313-321	9	22
β-strand	322	1	20
β-strand	327-333	7	22
α-helix	343-349	7
α-helix	350-355	6
β-strand	375-378	4	22

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)
TTL protein	F	protein	384	Gallus gallus	A0A8V0Z8P0 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5KX5_1 Tubulin alpha chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D), FASTA

>5KX5_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYSIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (E), FASTA

>5KX5_3 Stathmin-4 (chains E)
MADMEVIELNKATSGQSWEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRK
YQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLER
LQEKDKHAEEVRKNKELKEEASR

Sequence of entity 4 (F), FASTA

>5KX5_4 TTL protein (chains F)
MYTFVVRDENSSVYAEVSRLLLATGQWKRLRKDNPRFNLMLGERNRLPFGRLGHEPGLVQ
LVNYYRGADKLCRKASLVKLIKTSPELSESCTWFPESYVIYPTNLKTPVAPAQNGIRHLI
NNTRTDEREVFLAAYNRRREGREGNVWIAKSSAGAKGEGILISSEASELLDFIDEQGQVH
VIQKYLEKPLLLEPGHRKFDIRSWVLVDHLYNIYLYREGVLRTSSEPYNSANFQDKTCHL
TNHCIQKEYSKNYGRYEEGNEMFFEEFNQYLMDALNTTLENSILLQIKHIIRSCLMCIEP
AISTKHLHYQSFQLFGFDFMVDEELKVWLIEVNGAPACAQKLYAELCQGIVDVAISSVFP
LADTGQKTSQPTSIFIKLHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
6YK	(2~{S},4~{R})-4-[[2-[(1~{R},3~{R})-1-acetyloxy-3-[[(2~{S},3~{S})-2-[[(2~{R})-1,…	C38 H58 N6 O7 S	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
CA	Calcium ion	Ca	4
MG	Magnesium ion	Mg	6
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Primary citation

Design, Synthesis, and Cytotoxic Evaluation of Novel Tubulysin Analogues as ADC Payloads. Leverett, C.A., Sukuru, S.C., Vetelino, B.C. et al. ACS Med Chem Lett (2016) 7:999-1004. DOI 10.1021/acsmedchemlett.6b00274 · 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
6TDE 2.29 Å, Tubulin-inhibitor complex
3RYI 2.4 Å, GDP-Tubulin: rb3 stathmin-like domain 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 5KX5 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.