9YMG: Human KIF18A-DARPin fusion protein

Human KIF18A-DARPin fusion protein bound to AMP-PNP and tubulin. Determined by X-ray diffraction at 2.41 Å resolution. Released 5 Nov 2025.

Method: X-ray diffraction
Resolution: 2.41 Å
Organisms: Sus scrofa, Homo sapiens, synthetic construct
Chains: 6
Atoms: 21,620
Mol. weight: 322.69 kDa
Ligands: ANP, GDP, MG, GTP
Released: 5 Nov 2025

Explore 9YMG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9YMG contains 167 α-helices and 104 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: 31 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10-28	19
β-strand	35	1	2
α-helix	48-51	4
β-strand	53-56	4	2
β-strand	60-63	4	2
β-strand	65-69	5	1
α-helix	73-80	8
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-126	12
β-strand	132-140	9	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	206-216	11
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	278-280	3
α-helix	284-287	4
α-helix	288-293	6
α-helix	298-300	3
β-strand	301	1	3
α-helix	307-309	3
β-strand	312-321	10	3
α-helix	325-335	11
α-helix	336-338	3
β-strand	343	1	3
β-strand	352-356	5	3
α-helix	358-360	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: 27 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	5
α-helix	10-27	18
β-strand	30	1	6
β-strand	36	1	6
α-helix	41-43	3
α-helix	47-49	3
β-strand	51-53	3	7
β-strand	59-61	3	7
β-strand	63-67	5	5
α-helix	71-77	7
α-helix	82-84	3
α-helix	87-89	3
β-strand	90-92	3	5
α-helix	101-106	6
α-helix	113-125	13
β-strand	130-138	9	5
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-170	8	5
α-helix	173-175	3
α-helix	181-195	15
β-strand	198-203	6	5
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
α-helix	238-241	4
α-helix	250-257	8
β-strand	265-266	2	5
β-strand	267-271	5	8
α-helix	286-293	8
α-helix	296-298	3
β-strand	299	1	8
α-helix	305-307	3
β-strand	310-319	10	8
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	8
β-strand	349-354	6	8
α-helix	357-358	2
β-strand	363-371	9	8
α-helix	372-374	3
α-helix	375-391	17
α-helix	395-399	5
α-helix	406-427	22

Chain C: 26 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	9
α-helix	19-21	3
α-helix	23-28	6
α-helix	30-31	2
β-strand	32	1	10
β-strand	35-36	2	11
β-strand	41-43	3	11
β-strand	73-75	3	11
β-strand	78-80	3	9
α-helix	86-91	6
α-helix	95-97	3
α-helix	98-102	5
β-strand	107-112	6	9
α-helix	119-124	6
α-helix	132-146	15
β-strand	151-163	13	9
β-strand	166-169	4	9
β-strand	177	1	9
β-strand	179-182	4	12
β-strand	186-189	4	12
α-helix	192-194	3
β-strand	195	1	9
α-helix	200-213	14
β-strand	229-240	12	9
β-strand	250-258	9	9
α-helix	259-262	4
α-helix	273-295	23
α-helix	307-309	3
α-helix	311-315	5
α-helix	316-319	4
β-strand	325-332	8	9
β-strand	335	1	10
α-helix	339-352	14
α-helix	396-407	12
α-helix	410-418	9
α-helix	433-439	7
α-helix	443-450	8
α-helix	466-473	8
α-helix	476-484	9
α-helix	499-505	7
α-helix	509-517	9
α-helix	532-537	6
α-helix	542-547	6

Chain D: 30 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	13
α-helix	10-28	19
β-strand	35	1	14
α-helix	48-51	4
β-strand	53-56	4	14
β-strand	60-63	4	14
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	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-126	12
β-strand	132-140	9	13
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	13
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	13
α-helix	206-216	11
α-helix	224-243	20
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	15
β-strand	277	1	16
α-helix	278-280	3
α-helix	284-287	4
α-helix	288-293	6
α-helix	298-300	3
β-strand	301	1	15
α-helix	307-309	3
β-strand	312-321	10	15
α-helix	325-336	12
β-strand	343	1	15
β-strand	352-356	5	15
α-helix	358-360	3
β-strand	368	1	16
α-helix	369-370	2
β-strand	373-381	9	15
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	416-435	20

Chain E: 27 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	17
α-helix	10-27	18
β-strand	30	1	18
β-strand	36	1	18
α-helix	41-43	3
α-helix	47-49	3
β-strand	51-53	3	19
β-strand	59-61	3	19
β-strand	63-67	5	17
α-helix	71-77	7
α-helix	82-84	3
α-helix	87-89	3
β-strand	90-92	3	17
α-helix	101-105	5
α-helix	107-110	4
α-helix	113-125	13
β-strand	130-138	9	17
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-170	8	17
α-helix	181-195	15
β-strand	198-203	6	17
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
α-helix	238-241	4
α-helix	250-257	8
β-strand	265-266	2	17
β-strand	267-271	5	20
α-helix	286-293	8
α-helix	296-298	3
β-strand	299	1	20
α-helix	305-307	3
β-strand	310-319	10	20
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	20
β-strand	349-354	6	20
α-helix	357-358	2
β-strand	363-371	9	20
α-helix	372-374	3
α-helix	375-391	17
α-helix	395-399	5
α-helix	406-426	21

Chain F: 26 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	21
α-helix	19-21	3
α-helix	23-28	6
α-helix	30-31	2
β-strand	32	1	22
β-strand	34-36	3	23
β-strand	41-44	4	23
β-strand	72-75	4	23
β-strand	78-80	3	21
α-helix	86-91	6
α-helix	95-97	3
α-helix	98-102	5
β-strand	107-112	6	21
α-helix	119-124	6
α-helix	132-146	15
β-strand	151-163	13	21
β-strand	166-169	4	21
β-strand	177	1	21
β-strand	179-182	4	24
β-strand	186-189	4	24
α-helix	192-194	3
β-strand	195	1	21
α-helix	200-213	14
β-strand	229-240	12	21
β-strand	250-258	9	21
α-helix	259-262	4
α-helix	273-295	23
α-helix	307-309	3
α-helix	311-315	5
α-helix	317-319	3
β-strand	322	1	25
β-strand	325-332	8	21
β-strand	335	1	22
α-helix	339-352	14
β-strand	357	1	25
α-helix	397-407	11
α-helix	410-418	9
α-helix	433-439	7
α-helix	443-450	8
α-helix	466-473	8
α-helix	476-484	9
α-helix	499-505	7
α-helix	509-517	9
α-helix	532-538	7
α-helix	542-547	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A, D	protein	451	Sus scrofa	Q2XVP4 (AlphaFold model)
Tubulin beta chain	B, E	protein	444	Sus scrofa	P02554 (AlphaFold model)
Kinesin-like protein KIF18A, DARPin fusion protein	C, F	protein	555	Homo sapiens, synthetic construct	Q8NI77 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>9YMG_1 Tubulin alpha-1B chain (chains A, D)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, E), FASTA

>9YMG_2 Tubulin beta chain (chains B, E)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEEEDFGEEAEEEA

Sequence of entity 3 (C, F), FASTA

>9YMG_3 Kinesin-like protein KIF18A, DARPin fusion protein (chains C, F)
SNAMSVTEEDLCHHMKVVVRVRPENTKEKAAGFHKVVHVVDKHILVFDPKQEEVSFFHGK
KTTNQNVIKKQNKDLKFVFDAVFDETSTQSEVFEHTTKPILRSFLNGYNCTVLAYGATGA
GKTHTMLGSADEPGVMYLTMLHLYKCMDEIKEEKICSTAVSYLEVYNEQIRDLLVNSGPL
AVREDTQKGVVVHGLTLHQPKSSEEILHLLDNGNKNRTQHPTDMNATSSRSHAVFQIYLR
QQDKTASINQNVRIAKMSLIDLAGSERASTSGAKGTRFVEGTNINRSLLALGNVINALAD
SKRKNQHIPYRNSKLTRLLKDSLGGNCQTIMIAAVSPSSVFYDDTYNTLKYANRAKDIKS
SLKSNVLNVNGGGGSGGGGSGGGGSGGGGSGGGGSGGSDLGKKLLEAARAGQDDEVRILM
ANGADVNATDASGLTPLHLAATYGHLEIVEVLLKHGADVNAIDIMGSTPLHLAALIGHLE
IVEVLLKHGADVNAVDTWGDTPLHLAAIMGHLEIVEVLLKHGADVNAQDKFGKTAFDISI
DNGNEDLAEILQKLN

Ligands and cofactors

ID	Name	Formula	Copies
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
MG	Magnesium ion	Mg	6
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

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

Primary citation

Discovery of Kinesin KIF18A Inhibitor ATX020: Tactical Application of Silicon Atom Replacement. Sparling, B.A., Lee, H., Zablocki, M.M. et al. ACS Med Chem Lett (2025) 16:2309-2319. DOI 10.1021/acsmedchemlett.5c00512 · 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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