7CNM: YDX

YDX in complex with tubulin. Determined by X-ray diffraction at 2.44 Å resolution. Released 4 Aug 2021.

Method: X-ray diffraction
Resolution: 2.44 Å
Organisms: Sus scrofa, Mus musculus, Gallus gallus
Chains: 6
Atoms: 17,919
Mol. weight: 266.25 kDa
Ligands: GDP, CA, MG, GTP
Released: 4 Aug 2021

Explore 7CNM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7CNM contains 126 α-helices and 92 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: 28 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-28	19
β-strand	35	1	2
α-helix	48-51	4
β-strand	53-55	3	3
β-strand	60	1	2
β-strand	61-63	3	3
β-strand	65-69	5	1
α-helix	73-79	7
α-helix	89-91	3
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-126	16
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	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
β-strand	269-273	5	4
β-strand	277	1	5
α-helix	284-287	4
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	4
α-helix	307-309	3
β-strand	312-321	10	4
α-helix	325-338	14
α-helix	342	1
β-strand	343	1	4
α-helix	344	1
β-strand	349-356	8	4
α-helix	359-363	5
β-strand	368	1	5
α-helix	369-370	2
β-strand	373-381	9	4
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	416-436	21

Chain B: 26 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	6
α-helix	10-27	18
β-strand	30	1	7
β-strand	35	1	8
β-strand	36	1	7
α-helix	41-43	3
α-helix	47-49	3
β-strand	51-54	4	8
β-strand	58-61	4	8
β-strand	63-67	5	6
α-helix	71-78	8
α-helix	82-84	3
α-helix	87-89	3
β-strand	90-92	3	6
α-helix	101-105	5
α-helix	108-125	18
β-strand	132-138	7	6
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-170	8	6
α-helix	171	1
α-helix	181-195	15
β-strand	198-203	6	6
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-241	20
α-helix	250-257	8
β-strand	265-266	2	6
β-strand	267-271	5	9
α-helix	283-285	3
α-helix	286-293	8
α-helix	296-298	3
β-strand	299	1	9
α-helix	305-307	3
β-strand	310-318	9	9
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	9
β-strand	349-354	6	9
β-strand	364-371	8	9
α-helix	372-374	3
α-helix	375-389	15
α-helix	396-399	4
α-helix	405-426	22

Chain C: 31 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	10
α-helix	10-28	19
α-helix	48-51	4
β-strand	53-55	3	11
β-strand	61-63	3	11
β-strand	65-69	5	10
α-helix	73-80	8
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	10
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	10
α-helix	144	1
α-helix	145-149	5
α-helix	150-161	12
β-strand	165-172	8	10
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	10
α-helix	206-217	12
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	288-294	7
α-helix	298-300	3
β-strand	301	1	12
α-helix	307-309	3
β-strand	312-321	10	12
α-helix	325-338	14
β-strand	343	1	12
β-strand	352-356	5	12
α-helix	359-360	2
β-strand	368	1	13
α-helix	369-370	2
β-strand	373-381	9	12
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-436	22
α-helix	438-439	2

Chain D: 26 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	14
α-helix	10-28	19
β-strand	30	1	15
β-strand	35	1	16
β-strand	36	1	15
α-helix	41-43	3
α-helix	47-49	3
β-strand	51-54	4	16
β-strand	58-61	4	16
β-strand	63-67	5	14
α-helix	71-78	8
α-helix	82-84	3
α-helix	87-89	3
β-strand	90-92	3	14
α-helix	101-105	5
α-helix	108-125	18
β-strand	130-138	9	14
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-170	8	14
α-helix	171	1
α-helix	181-195	15
β-strand	198-203	6	14
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-241	20
α-helix	250-257	8
β-strand	265-266	2	14
β-strand	267-271	5	17
α-helix	286-293	8
α-helix	296-298	3
β-strand	299	1	17
α-helix	305-307	3
β-strand	310-319	10	17
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	17
β-strand	349-354	6	17
α-helix	357-358	2
β-strand	363-371	9	17
α-helix	372-374	3
α-helix	375-390	16
α-helix	396-399	4
α-helix	406-427	22

Chain E: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	4
β-strand	18-25	8	4
α-helix	47-139	93

Chain F: 14 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	18
α-helix	12-23	12
β-strand	27-29	3	18
β-strand	39-41	3	18
α-helix	49-51	3
β-strand	61-62	2	18
α-helix	69-72	4
α-helix	74-83	10
β-strand	97-100	4	19
α-helix	128-141	14
β-strand	147-148	2	19
β-strand	163	1	19
α-helix	166-176	11
β-strand	180-184	5	19
β-strand	189	1	20
β-strand	192	1	21
β-strand	197	1	21
β-strand	199-207	9	22
β-strand	213-216	4	22
β-strand	220-223	4	22
α-helix	258-260	3
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	336-339	4
α-helix	343-350	8
α-helix	351-355	5
β-strand	375-377	3	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A, C	protein	451	Sus scrofa	Q2XVP4 (AlphaFold model)
Tubulin beta chain	B, D	protein	445	Sus scrofa	A0A8D1UIR5 (AlphaFold model)
Stathmin-4	E	protein	143	Mus musculus	P63042 (AlphaFold model)
Tubulin tyrosine ligase	F	protein	384	Gallus gallus	A0A8V0Z8P0 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7CNM_1 Tubulin alpha-1B chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D), FASTA

>7CNM_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (E), FASTA

>7CNM_3 Stathmin-4 (chains E)
MADMEVIELNKCTSGQSFEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRK
YQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLER
LQEKDKHAEEVRKNKELKEEASR

Sequence of entity 4 (F), FASTA

>7CNM_4 Tubulin tyrosine ligase (chains F)
MYTFVVRDENSSVYAEVSRLLLATGQWKRLRKDNPRFNLMLGERNRLPFGRLGHEPGLVQ
LVNYYRGADKLCRKASLVKLIKTSPELSESCTWFPESYVIYPTNLKTPVAPAQNGIRHLI
NNTRTDEREVFLAAYNRRREGREGNVWIAKSSAGAKGEGILISSEASELLDFIDEQGQVH
VIQKYLEKPLLLEPGHRKFDIRSWVLVDHLYNIYLYREGVLRTSSEPYNSANFQDKTCHL
TNHCIQKEYSKNYGRYEEGNEMFFEEFNQYLMDALNTTLENSILLQIKHIIRSCLMCIEP
AISTKHLHYQSFQLFGFDFMVDEELKVWLIEVNGAPACAQKLYAELCQGIVDVAISSVFP
LADTGQKTSQPTSIFIKLHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
CA	Calcium ion	Ca	2
MG	Magnesium ion	Mg	3
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
ACP	Phosphomethylphosphonic acid adenylate ester	C11 H18 N5 O12 P3	1
G70	(2~{S},4~{S})-4-[[2-[(1~{R},3~{R})-1-acetyloxy-4-methyl-3-[[(2~{S},3~{S})-3-met…	C37 H61 N5 O7 S	2

Water and common crystallization additives (MES) are not listed.

Primary citation

The high-resolution X-ray structure of vinca-domain inhibitors of microtubules provides a rational approach for drug design. Chengyong, W., Jinghong, X., Yanyan, W. et al. FEBS Lett (2021) 595:195-205. DOI 10.1002/1873-3468.14003 · PubMed

Other PDB entries of the same protein (UniProt Q2XVP4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9U6A 1.92 Å, Tubulin-DARPin D1 in complex with a flavone
5EZY 2.05 Å, Crystal structure of T2R-TTL-taccalonolide AJ complex
5YL2 2.09 Å, Crystal structure of T2R-TTL-Y28 complex
7TTF 2.1 Å, Tubulin-RB3_SLD in complex with compound 12k
5XKG 2.2 Å, Crystal structure of T2R-TTL-CH1 complex
7L05 2.21 Å, Complex of novel maytansinoid M24 bound to T2R-TTL (two tubulin alpha/beta heterodimers,…
9M1M 2.21 Å, Cryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
5JQG 2.24 Å, An apo tubulin-RB-TTL complex structure used for side-by-side comparison
9M1N 2.24 Å, Cryo-EM structure of the TBC-DC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
5XKH 2.25 Å, Crystal structure of T2R-TTL-CF1 complex
7TTD 2.27 Å, Tubulin-RB3_SLD in complex with compound 12e
5JCB 2.3 Å, Microtubule depolymerizing agent podophyllotoxin derivative YJTSF1

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