4X1K: Tubulin alpha chain

Discovery of cytotoxic Dolastatin 10 analogs with N-terminal modifications. Determined by X-ray diffraction at 3.5 Å resolution. Released 25 Mar 2015.

Method: X-ray diffraction
Resolution: 3.5 Å
Organisms: Ovis aries, Rattus norvegicus
Chains: 5
Atoms: 14,713
Mol. weight: 221.22 kDa
Ligands: GTP, MG, GDP, LOC
Released: 25 Mar 2015

Explore 4X1K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4X1K contains 93 α-helices and 83 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: 21 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	1
α-helix	12-27	16
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	73-76	4
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	134-139	6	1
α-helix	145-160	16
β-strand	165-172	8	1
α-helix	183-194	12
β-strand	200-205	6	1
α-helix	206-215	10
α-helix	224-243	20
α-helix	253-258	6
β-strand	269-270	2	3
β-strand	271	1	4
β-strand	273	1	5
β-strand	277	1	6
α-helix	284-286	3
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	4
β-strand	312	1	7
β-strand	316	1	3
β-strand	318-321	4	5
α-helix	325-338	14
β-strand	343	1	7
β-strand	349-356	8	5
α-helix	359-361	3
β-strand	368	1	6
β-strand	373-375	3	5
β-strand	378-379	2	3
β-strand	381	1	7
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	416-435	20

Chain B: 24 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	8
α-helix	10-27	18
β-strand	30	1	9
β-strand	36	1	9
α-helix	42-47	4
β-strand	53-55	3	10
β-strand	61-63	3	10
β-strand	65-69	5	8
α-helix	73-80	8
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	8
α-helix	103-107	5
α-helix	109-127	19
β-strand	134-140	7	8
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	8
α-helix	173	1
α-helix	183-197	15
β-strand	200-205	6	8
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	8
β-strand	269-271	3	11
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	11
β-strand	312-320	9	11
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	11
β-strand	351-354	4	11
β-strand	374-381	8	11
α-helix	382-384	3
α-helix	385-400	16
α-helix	406-409	4
α-helix	415-436	22

Chain C: 21 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	12
α-helix	12-27	16
α-helix	48-51	4
β-strand	53-55	3	13
β-strand	61-63	3	13
β-strand	65-69	5	12
α-helix	72-79	8
β-strand	92-94	3	12
α-helix	103-107	5
α-helix	112-126	15
β-strand	132-140	9	12
α-helix	144-149	6
α-helix	150-160	11
β-strand	165-166	2	12
β-strand	169-172	4	12
α-helix	183-194	12
β-strand	202-205	4	12
α-helix	206-215	10
α-helix	224-243	20
α-helix	254-259	6
α-helix	268	1
β-strand	269	1	14
α-helix	270	1
β-strand	273	1	15
β-strand	277	1	16
α-helix	288-294	7
α-helix	298-300	3
β-strand	312	1	17
β-strand	316-319	4	18
β-strand	320	1	19
α-helix	325-337	13
β-strand	343	1	17
β-strand	352-355	4	18
β-strand	368	1	16
α-helix	369-370	2
β-strand	374	1	19
β-strand	375	1	15
β-strand	377-378	2	18
β-strand	379	1	14
β-strand	381	1	17
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	417-435	19

Chain D: 26 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	20
α-helix	10-26	17
β-strand	30	1	21
β-strand	35	1	22
β-strand	36	1	21
α-helix	42-47	4
β-strand	53-55	3	23
β-strand	60	1	22
β-strand	61-63	3	23
β-strand	65-69	5	20
α-helix	72-79	8
α-helix	83-85	3
α-helix	89-91	3
β-strand	92-94	3	20
α-helix	103-104	2
α-helix	105-109	5
α-helix	110-127	18
β-strand	132-140	9	20
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	20
α-helix	183-197	15
β-strand	200-205	6	20
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	20
β-strand	269-270	2	24
β-strand	273	1	24
α-helix	285-287	3
α-helix	288-295	8
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-320	9	24
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	24
β-strand	351-356	6	24
α-helix	359-360	2
β-strand	375-381	7	24
α-helix	382-384	3
α-helix	385-400	16
α-helix	406-409	4
α-helix	416-437	22

Chain E: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	12-14	3	5
β-strand	17-25	9	5
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	142	Rattus norvegicus	P63043 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4X1K_1 Tubulin alpha chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D), FASTA

>4X1K_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYSIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (E), FASTA

>4X1K_3 Stathmin-4 (chains E)
ADMEVIELNKATSGQSWEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKY
QEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERL
QEKDKHAEEVRKNKELKEEASR

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
MG	Magnesium ion	Mg	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	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
3WZ	2-methyl-L-alanyl-N-[(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(1S)-1-carboxy-2-phenyle…	C37 H61 N5 O8	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…

Browse structure collections

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