9KKJ: Nectin-4 D1 domain

Structure of Nectin-4 D1 domain in complex with the Fab fragment of 9MW2821 mAb. Determined by electron microscopy at 3.26 Å resolution. Released 19 Nov 2025.

Method: Electron microscopy
Resolution: 3.26 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 4,126
Mol. weight: 59.56 kDa
Released: 19 Nov 2025

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

Secondary structure: helices and β-sheets

9KKJ contains 11 α-helices and 66 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: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	16
β-strand	39-40	2	17
β-strand	48-50	3	18
β-strand	53-54	2	16
β-strand	62-70	9	17
β-strand	76-83	8	17
β-strand	87-90	4	17
β-strand	98-99	2	18
α-helix	100-101	2
β-strand	109	1	16
β-strand	112-114	3	18
α-helix	119-121	3
β-strand	123-131	9	17
β-strand	139-143	5	17

Chain H: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	8
β-strand	12-13	2	9
β-strand	17-19	3	8
β-strand	22-26	5	8
β-strand	35-40	6	10
β-strand	47-52	6	10
β-strand	58-60	3	10
β-strand	68-73	6	8
β-strand	78-86	9	8
α-helix	88-90	3
β-strand	92-99	8	10
β-strand	107-110	4	10
β-strand	114-116	3	10
β-strand	117-118	2	9
α-helix	124-126	3
β-strand	127	1	11
β-strand	131	1	12
β-strand	142-143	2	13
β-strand	146-147	2	12
β-strand	150-152	3	11
β-strand	158-160	3	14
β-strand	161	1	15
β-strand	166	1	15
β-strand	170-172	3	12
α-helix	173-175	3
β-strand	176-177	2	11
β-strand	183-184	2	11
β-strand	187-189	3	12
β-strand	191-192	2	13
α-helix	194-196	3
β-strand	201-207	7	14
α-helix	208-210	3
β-strand	212-218	7	14

Chain L: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	30-31	2	3
β-strand	36-37	2	3
β-strand	39-42	4	4
β-strand	44	1	2
β-strand	52-54	3	4
β-strand	60	1	4
β-strand	68	1	1
β-strand	71-73	3	1
β-strand	76-81	6	1
β-strand	91-92	2	2
β-strand	94-96	3	4
β-strand	103-104	2	4
β-strand	108-112	5	2
β-strand	117	1	5
α-helix	118-120	3
β-strand	121-124	4	6
α-helix	125-127	3
α-helix	128-133	6
β-strand	135-145	11	6
β-strand	146	1	5
β-strand	152-156	5	7
β-strand	159-161	3	7
β-strand	165-170	6	6
β-strand	179-188	10	6
α-helix	189-192	4
β-strand	197-202	6	7
β-strand	211-216	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
9MW2821 mAb Fab Light chain	L	protein	218	Mus musculus
9MW2821 mAb Fab Heavy Chain	H	protein	220	Mus musculus
Nectin-4	A	protein	114	Homo sapiens	Q96NY8 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>9KKJ_1 9MW2821 mAb Fab Light chain (chains L)
DIVMTQSPDSLAVSLGERATINCKSSQSLLNTYSQKNYLAWYQQKPGQPPKLLIYFASTR
ESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQHYNTPFTFGGGTKVEIKRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Sequence of entity 2 (H), FASTA

>9KKJ_2 9MW2821 mAb Fab Heavy Chain (chains H)
EVQLQESGPGLVKPSETLSLTCTVSGFSLIDYGVSWIRQPPGKGLEWIGVIWGGGKIYYN
SVLKSRVTISKDNSKSQVSLKLSSVTAADTAVYYCAKQGGLLFYAMDYWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK

Sequence of entity 3 (A), FASTA

>9KKJ_3 Nectin-4 (chains A)
GELETSDVVTVVLGQDAKLPCFYRGDSGEQVGQVAWARVDAGEGAQELALLHSKYGLHVS
PAYEGRVEQPPPPRNPLDGSVLLRNAVQADEGEYECRVSTFPAGSFQARLRLRV

Primary citation

Structural basis of nectin-4 recognition by the antibody-drug conjugate 9MW2821. Fang, P., You, M., Wen, H. et al. J Biol Chem (2025) 301:110816-110816. DOI 10.1016/j.jbc.2025.110816 · PubMed

Other PDB entries of the same protein (UniProt Q96NY8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4JJH 2.25 Å, Crystal structure of the D1 domain from human Nectin-4 extracellular fragment…
9UCL 2.43 Å, CryoEM structure of IgV domain of human Nectin-4 with Trimbody
4GJT 3.1 Å, complex structure of nectin-4 bound to MV-H
4FRW 3.5 Å, Crystal structure of human nectin-4 extracellular fragment D1-D2

Browse structure collections

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