6H9B: Tubulin alpha chain

1,1-Diheterocyclic Ethylenes Derived from Quinaldine and Carbazole as New Tubulin Polymerization Inhibitors: Synthesis, Metabolism, and Biological Evaluation. Determined by X-ray diffraction at 2.75 Å resolution. Released 19 Dec 2018.

Method: X-ray diffraction
Resolution: 2.75 Å
Organisms: Ovis aries, Rattus norvegicus
Chains: 5
Atoms: 15,108
Mol. weight: 214.03 kDa
Ligands: FWH, GDP, MG, GTP
Released: 19 Dec 2018

Explore 6H9B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6H9B contains 116 α-helices and 71 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: 30 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	65-69	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	111-127	17
β-strand	134-140	7	1
α-helix	144	1
α-helix	145-149	5
α-helix	150-161	12
β-strand	165-172	8	1
α-helix	175-177	3
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	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: 27 helices, 18 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	42-47	4
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	84-86	3
α-helix	89-91	3
β-strand	92-94	3	5
α-helix	103-108	6
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	175-177	3
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	288-293	6
α-helix	298-300	3
β-strand	301	1	8
α-helix	307-309	3
β-strand	312-320	9	8
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	8
β-strand	351-356	6	8
α-helix	359-360	2
β-strand	374-381	8	8
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	415-437	23

Chain C: 31 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	9
α-helix	10-28	19
α-helix	48-51	4
β-strand	53-55	3	10
β-strand	61-63	3	10
β-strand	65-69	5	9
α-helix	73-80	8
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	115-126	12
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	175-177	3
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	9
α-helix	206-215	10
α-helix	224-243	20
β-strand	247	1	11
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	11
β-strand	277	1	12
α-helix	288-293	6
α-helix	294-296	3
α-helix	298-300	3
β-strand	301	1	11
α-helix	307-309	3
β-strand	312-321	10	11
α-helix	325-336	12
α-helix	342	1
β-strand	343	1	11
α-helix	344	1
β-strand	351-356	6	11
α-helix	359-361	3
β-strand	368	1	12
α-helix	369-370	2
β-strand	373-381	9	11
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	415-435	21

Chain D: 27 helices, 18 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	42-47	4
α-helix	49-51	3
β-strand	53-56	4	15
β-strand	60-63	4	15
β-strand	65-69	5	13
α-helix	73-80	8
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	13
α-helix	103-108	6
α-helix	110-127	18
β-strand	132-140	9	13
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	13
α-helix	173	1
α-helix	175-177	3
α-helix	183-197	15
β-strand	200-205	6	13
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	13
β-strand	269-273	5	16
α-helix	288-293	6
α-helix	298-300	3
β-strand	301	1	16
α-helix	307-309	3
β-strand	312-321	10	16
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	16
β-strand	351-356	6	16
α-helix	359-360	2
β-strand	373-381	9	16
α-helix	382-384	3
α-helix	385-400	16
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	47-138	92

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha chain	A, C	protein	433	Ovis aries	D0VWZ0 (AlphaFold model)
Tubulin beta chain	B, D	protein	431	Ovis aries	D0VWY9 (AlphaFold model)
Stathmin-4	E	protein	142	Rattus norvegicus	P63043 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6H9B_1 Tubulin alpha chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDDSFNTFFSETGAGKHVPRAVF
VDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLAD
QCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNS
ILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGA
LNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDP
RHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGD
LAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAA
LEKDYEEVGVDSV

Sequence of entity 2 (B, D), FASTA

>6H9B_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVATIFRGRMSMKEVDEQMLNIQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAD

Sequence of entity 3 (E), FASTA

>6H9B_3 Stathmin-4 (chains E)
ADMEVIELNKATSGQSWEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKY
QEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERL
QEKDKHAEEVRKNKELKEEASR

Ligands and cofactors

ID	Name	Formula	Copies
FWH	9-methyl-3-[1-(2-methylquinolin-4-yl)ethenyl]carbazole	C25 H20 N2	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

1,1-Diheterocyclic Ethylenes Derived from Quinaldine and Carbazole as New Tubulin-Polymerization Inhibitors: Synthesis, Metabolism, and Biological Evaluation. Naret, T., Khelifi, I., Provot, O. et al. J Med Chem (2019) 62:1902-1916. DOI 10.1021/acs.jmedchem.8b01386 · 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
3RYH 2.8 Å, GMPCPP-Tubulin: RB3 Stathmin-like domain complex

Browse structure collections

About this viewer

MolViewer shows 6H9B 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.