9YTD: PDB entry 9YTD

Designed antibody vAB66 targeting PAP-HLA A*02:01. Determined by electron microscopy at 2.5 Å resolution. Released 17 Dec 2025.

Method: Electron microscopy
Resolution: 2.5 Å
Organisms: Homo sapiens, Lama glama, synthetic construct
Chains: 6
Atoms: 7,368
Mol. weight: 105.79 kDa
Released: 17 Dec 2025

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

Secondary structure: helices and β-sheets

9YTD contains 27 α-helices and 86 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-150	13
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
β-strand	186-194	9	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	213-219	7	4
β-strand	222-223	2	4
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
β-strand	257-263	7	4
β-strand	270-273	4	4

Chain B: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	35-41	7	7
β-strand	45	1	7
β-strand	50-51	2	6
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-84	7	7
β-strand	91-94	4	7

Chain D: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	8
β-strand	12-14	3	9
β-strand	20-27	8	8
α-helix	30-32	3
β-strand	35-41	7	9
β-strand	47-53	7	9
β-strand	59-61	3	9
α-helix	63-65	3
β-strand	66	1	8
β-strand	69-74	6	8
β-strand	79-84	6	8
α-helix	89-91	3
β-strand	93-100	8	9
β-strand	106-108	3	9
β-strand	112-116	5	9

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	34-39	7	12
β-strand	46-51	6	12
β-strand	57-59	3	12
α-helix	64-66	3
β-strand	67-72	6	10
β-strand	77-82	6	10
α-helix	84-86	3
β-strand	88-95	8	12
β-strand	100-103	4	12
β-strand	107-109	3	12
β-strand	110-111	2	11
α-helix	115-116	2
β-strand	117	1	13
β-strand	120-124	5	14
α-helix	128-130	3
β-strand	135-145	11	14
β-strand	146	1	13
β-strand	151-154	4	15
α-helix	155-157	3
β-strand	159	1	15
β-strand	163-165	3	14
α-helix	166-168	3
β-strand	169-170	2	14
β-strand	176-185	10	14
α-helix	186-188	3
β-strand	194-200	7	15
β-strand	205-211	7	15

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-14	5	17
β-strand	19-25	7	16
β-strand	33-38	6	17
β-strand	45-49	5	17
β-strand	53-54	2	17
α-helix	55	1
β-strand	62-67	6	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	84-90	7	17
β-strand	97-98	2	17
β-strand	102-107	6	17
β-strand	111	1	18
α-helix	112-113	2
β-strand	114-118	5	19
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	19
β-strand	140	1	18
β-strand	144-150	7	20
β-strand	154	1	20
β-strand	159-163	5	19
α-helix	164-167	4
β-strand	173-182	10	19
α-helix	183-186	4
β-strand	191-198	8	20
β-strand	205-210	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A alpha chain	A	protein	279	Homo sapiens	A5I8L1 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Prostatic acid phosphatase-derived peptide	C	protein	9	Homo sapiens	P15309 (AlphaFold model)
AD01 nanobody	D	protein	127	Lama glama
vAB66 heavy chain	H	protein	218	synthetic construct
vAB66 light chain	L	protein	217	synthetic construct

Sequence of entity 1 (A), FASTA

>9YTD_1 HLA class I histocompatibility antigen, A alpha chain (chains A)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEPSS

Sequence of entity 2 (B), FASTA

>9YTD_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>9YTD_3 Prostatic acid phosphatase-derived peptide (chains C)
TLMSAMTNL

Sequence of entity 4 (D), FASTA

>9YTD_4 AD01 nanobody (chains D)
EVKLVESGGGLVQPGGSLRLSCAASGSIFSINTMGWYRQTPGKQRDLVADISSGGSTKYG
DSVKGRFTISRDNTKNTVYLQMNSLKPEDTAVYYCYGLSYSNDDYWGQGTQVTVSSGAPH
HHHHHHH

Sequence of entity 5 (H), FASTA

>9YTD_5 vAB66 heavy chain (chains H)
QVQLQESGPGLVKPSETLSLTCAVSNAKLTEYDWWGWIRQPPGKGLEWIGSGNAYGLVYY
NPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARYDGVVLYPWGQGTLVTVSSAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 6 (L), FASTA

>9YTD_6 vAB66 light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASADPQGFLNWYQQKPGKAPKLLIYLASSLQSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQSWSERGPYLTFGGGTKVEIKRTVAAPSVFI
FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Targeting peptide-MHC complexes with designed T cell receptors and antibodies. Motmaen, A., Jude, K.M., Wang, N. et al. bioRxiv (2025). DOI 10.1101/2025.11.19.689381 · PubMed

Other PDB entries of the same protein (UniProt A5I8L1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9SKO 1.49 Å, Crystal structure of HLA-A0201 in complex with peptide LLWNGPMAVS
9SL0 1.6 Å, Crystal structure of HLA-A0201 in complex with peptide LLWNGPMAV
9SKP 1.89 Å, Crystal structure of HLA-A0201 in complex with peptide SLLWNGPMAV
9NMV 1.97 Å, TCR156 S32Halpha bound to HLA A*02:01-PAP
9NMY 2.01 Å, TCR156 S32Qalpha bound to HLA A*02:01-PAP
9T2A 2.04 Å, Human Single Domain TCR-like Antibody 6K23 in complex with NY-ESO-1(C165V):HLA-A0201
9NMU 2.1 Å, TCR156 bound to HLA A*02:01-PAP
9NMW 2.11 Å, TCR156 S30Ealpha S32Qalpha bound to HLA A*02:01-PAP
9NMX 2.19 Å, TCR156 S32Malpha variant bound to HLA A*02:01-PAP
9O5S 2.27 Å, minibinder-antigen complex BXMart1-3-MART1-HLA*A02
9T2B 2.34 Å, Human Single Domain TCR-like Antibody 5F17 in complex with NY-ESO-1(C165V):HLA-A0201
9T2C 2.89 Å, Human Single Domain TCR-like Antibody A10 in complex with NY-ESO-1(C165V):HLA-A0201

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