4X1Y: Tubulin alpha chain

Discovery of cytotoxic Dolastatin 10 analogs with N-terminal modifications. Determined by X-ray diffraction at 3.19 Å resolution. Released 25 Mar 2015.

Method: X-ray diffraction
Resolution: 3.19 Å
Organisms: Ovis aries, Rattus norvegicus
Chains: 5
Atoms: 14,715
Mol. weight: 221.25 kDa
Ligands: 3WV, LOC, GDP, MG
Released: 25 Mar 2015

Explore 4X1Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4X1Y contains 98 α-helices and 72 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: 22 helices, 18 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	72-78	7
α-helix	82-84	3
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	110-126	17
β-strand	132-140	9	1
α-helix	145-160	16
β-strand	165-172	8	1
α-helix	183-193	11
β-strand	200-205	6	1
α-helix	206-215	10
α-helix	224-243	20
α-helix	252-254	3
α-helix	255-258	4
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	1	5
β-strand	316-321	6	3
α-helix	325-338	14
β-strand	343	1	5
β-strand	349-356	8	3
β-strand	368	1	4
β-strand	373-379	7	3
β-strand	381	1	5
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	415-435	21

Chain B: 27 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	6
α-helix	10-27	18
β-strand	30	1	7
β-strand	36	1	7
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-54	2	8
β-strand	62-63	2	8
β-strand	65-69	5	6
α-helix	73-80	8
α-helix	83-86	4
α-helix	89-91	3
β-strand	92-94	3	6
α-helix	103-104	2
α-helix	105-109	5
α-helix	110-127	18
β-strand	134-140	7	6
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	6
α-helix	173	1
α-helix	183-197	15
β-strand	200-205	6	6
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	6
β-strand	269-270	2	9
β-strand	273	1	9
α-helix	288-296	9
α-helix	298-300	3
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
β-strand	375-381	7	9
α-helix	382-384	3
α-helix	385-400	16
α-helix	406-409	4
α-helix	415-437	23

Chain C: 23 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	10
α-helix	10-27	18
α-helix	48-51	4
β-strand	53-55	3	11
β-strand	61-63	3	11
β-strand	65-68	4	10
α-helix	73-79	7
α-helix	89-91	3
β-strand	92	1	10
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-127	13
β-strand	132-140	9	10
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	10
α-helix	183-194	12
β-strand	200-205	6	10
α-helix	206-215	10
α-helix	224-243	20
α-helix	254-259	6
β-strand	269	1	12
β-strand	273	1	12
β-strand	277	1	13
α-helix	281-283	3
α-helix	288-294	7
α-helix	298-300	3
β-strand	312-320	9	12
α-helix	325-337	13
β-strand	343	1	12
β-strand	352-356	5	12
α-helix	359-363	5
β-strand	368	1	13
β-strand	374-381	8	12
α-helix	385-400	16
α-helix	405-409	5
α-helix	416-435	20

Chain D: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	14
α-helix	10-27	18
β-strand	30	1	15
β-strand	35	1	16
β-strand	36	1	15
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-55	3	17
β-strand	60	1	16
β-strand	61-63	3	17
β-strand	65-69	5	14
α-helix	73-80	8
α-helix	84-86	3
β-strand	92-94	3	14
α-helix	103-107	5
α-helix	110-128	19
β-strand	132-140	9	14
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	14
α-helix	183-197	15
β-strand	200-205	6	14
α-helix	206-215	10
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	18
α-helix	285-287	3
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
β-strand	374-381	8	18
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-407	3
α-helix	409-411	3
α-helix	415-437	23

Chain E: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	12-14	3	3
β-strand	17-25	9	3
α-helix	47-139	93

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	142	Rattus norvegicus	P63043 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4X1Y_1 Tubulin alpha chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D), FASTA

>4X1Y_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYSIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (E), FASTA

>4X1Y_3 Stathmin-4 (chains E)
ADMEVIELNKATSGQSWEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKY
QEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERL
QEKDKHAEEVRKNKELKEEASR

Ligands and cofactors

ID	Name	Formula	Copies
3WV	N,2-dimethyl-L-alanyl-N-[(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(1S)-1-carboxy-2-phe…	C38 H63 N5 O8	2
LOC	N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethana…	C22 H25 N O6	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

Primary citation

Discovery of cytotoxic dolastatin 10 analogues with N-terminal modifications. Maderna, A., Doroski, M., Subramanyam, C. et al. J Med Chem (2014) 57:10527-10543. DOI 10.1021/jm501649k · 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
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…

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