6S8L: Tubulin alpha-1B chain

Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes. Determined by X-ray diffraction at 1.8 Å resolution. Released 27 Nov 2019.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 8,691
Mol. weight: 118.7 kDa
Ligands: GTP, MG, PN6, GDP
Released: 27 Nov 2019

Explore 6S8L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6S8L contains 64 α-helices and 35 β-strands across 3 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: 28 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	103-107	5
α-helix	111-113	3
α-helix	115-127	13
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	175-177	3
α-helix	183-195	13
β-strand	200-205	6	1
α-helix	206-215	10
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	283-287	5
α-helix	288-293	6
α-helix	294-296	3
α-helix	298-300	3
β-strand	301	1	3
α-helix	307-309	3
β-strand	312-321	10	3
α-helix	325-336	12
β-strand	343	1	3
β-strand	352-356	5	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	416-435	20

Chain B: 26 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	5
α-helix	10-28	19
β-strand	30	1	6
β-strand	36	1	6
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-55	3	7
β-strand	61-63	3	7
β-strand	65-69	5	5
α-helix	73-79	7
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	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	224-243	20
α-helix	252-259	8
β-strand	267-268	2	5
β-strand	269-273	5	9
α-helix	288-296	9
α-helix	298-300	3
β-strand	301	1	9
α-helix	307-309	3
β-strand	312-320	9	9
α-helix	325-337	13
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	385-400	16
α-helix	405-409	5
α-helix	415-437	23

Chain F: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	14-24	11
α-helix	27-35	9
α-helix	50-56	7
α-helix	60-68	9
α-helix	83-90	8
α-helix	93-101	9
α-helix	116-122	7
α-helix	126-134	9
α-helix	149-155	7
α-helix	159-165	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A	protein	451	Homo sapiens	P68363 (AlphaFold model)
Tubulin beta-3 chain	B	protein	450	Homo sapiens	Q13509 (AlphaFold model)
Designed ankyrin repeat protein (DARPIN) D1	F	protein	157	synthetic construct

Sequence of entity 1 (A), FASTA

>6S8L_1 Tubulin alpha-1B chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>6S8L_2 Tubulin beta-3 chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYV
PRAILVDLEPGTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKECENCDCLQGFQLTHSLGGGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSIHQLVENTDETYCIDNEALYDICFRTLKLATPTYGDLNHLVSATMSGVTTSL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTARGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRG
LKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAEEEGEMYEDDEEESEAQGPK

Sequence of entity 3 (F), FASTA

>6S8L_3 Designed ankyrin repeat protein (DARPIN) D1 (chains F)
DLGKKLLEAARAGQDDEVRILMANGADVNATDASGLTPLHLAATYGHLEIVEVLLKHGAD
VNAIDIMGSTPLHLAALIGHLEIVEVLLKHGADVNAVDTWGDTPLHLAAIMGHLEIVEVL
LKHGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	2
PN6	(3Z,6Z)-3-benzylidene-6-[(5-tert-butyl-1H-imidazol-4-yl)methylidene]piperazine-…	C19 H20 N4 O2	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

Primary citation

Structure, Thermodynamics, and Kinetics of Plinabulin Binding to Two Tubulin Isotypes. La Sala, G., Olieric, N. Chem (2019). DOI 10.1016/j.chempr.2019.08.022

Other PDB entries of the same protein (UniProt P68363 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6J8O 1.85 Å, Structure of a hypothetical protease
7PJF 1.86 Å, Inhibiting parasite proliferation using a rationally designed anti-tubulin agent
6J4V 2.1 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
8VT7 2.66 Å, Structure of the gamma tubulin ring complex nucleated microtubule protofilament.
7Z6S 2.9 Å, MATCAP bound to a human 14 protofilament microtubule
8V2J 2.9 Å, Structure of alpha1B and betaI/IVb microtubule bound to GDP
9COC 2.9 Å, Two protofilament structure of alpha1B and betaI/IVb microtubule bound to GDP
9BP6 3.1 Å, Structure of alpha1B and betaI/IVb microtubule bound to GMPCPP
9CMM 3.1 Å, Two protofilament structure of alpha1B and betaI/IVb microtubule bound to GMPCPP
7LXB 3.26 Å, HeLa-tubulin in complex with cryptophycin 52
9HQ4 3.28 Å, TTLL11 bound to microtubule
7M18 3.38 Å, HeLa-tubulin in complex with cryptophycin 1

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