9O5S: PDB entry 9O5S

minibinder-antigen complex BXMart1-3-MART1-HLA*A02. Determined by X-ray diffraction at 2.27 Å resolution. Released 23 Jul 2025.

Method: X-ray diffraction
Resolution: 2.27 Å
Organisms: Homo sapiens, synthetic construct
Chains: 20
Atoms: 20,183
Mol. weight: 282.96 kDa
Released: 23 Jul 2025

Explore 9O5S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9O5S contains 74 α-helices and 163 β-strands across 16 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: 11 helices, 17 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	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
α-helix	183-185	3
β-strand	186-192	7	2
β-strand	198-208	11	2
β-strand	214-219	6	3
β-strand	222-223	2	3
β-strand	228-230	3	2
α-helix	231-233	3
β-strand	234-235	2	2
β-strand	241-250	10	2
α-helix	254-256	3
β-strand	257-262	6	3
β-strand	270-272	3	3

Chains B and M: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	4
α-helix	4-5	2
β-strand	6-11	6	5
β-strand	19	1	6
β-strand	21-30	10	5
β-strand	31	1	4
β-strand	36-41	6	7
β-strand	44-45	2	7
β-strand	50-51	2	5
α-helix	52-54	3
β-strand	55-56	2	5
β-strand	62-70	9	5
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain C: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	10
α-helix	20	1
β-strand	21-28	8	10
β-strand	31-37	7	10
β-strand	46-47	2	10
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	10
β-strand	109-118	10	10
β-strand	121-126	6	10
β-strand	133-135	3	10
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	11
α-helix	184-185	2
β-strand	186-192	7	12
β-strand	198-208	11	12
β-strand	209	1	11
β-strand	214-219	6	13
β-strand	222-223	2	13
β-strand	228-230	3	12
α-helix	231-233	3
β-strand	234-235	2	12
β-strand	241-250	10	12
α-helix	254-256	3
β-strand	257-262	6	13
β-strand	270-272	3	13

Chains D and I: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	20
α-helix	4-5	2
β-strand	6-11	6	21
β-strand	21-30	10	21
β-strand	31	1	20
β-strand	36-41	6	22
β-strand	44-45	2	22
β-strand	50-51	2	21
α-helix	52-54	3
β-strand	55-56	2	21
β-strand	62-70	9	21
β-strand	78-83	6	22
β-strand	91-94	4	22

Chain F: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	29
β-strand	12-14	3	30
β-strand	20-28	9	29
β-strand	33-41	9	30
α-helix	46-47	2
β-strand	48-53	6	30
β-strand	59-61	3	30
β-strand	66	1	29
β-strand	69-74	6	29
β-strand	79-84	6	29
α-helix	89-91	3
β-strand	93-101	9	30
β-strand	106-108	3	30
β-strand	112-116	5	30

Chain G: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	8
β-strand	12-14	3	9
β-strand	20-28	9	8
β-strand	33-41	9	9
α-helix	46	1
β-strand	47-53	7	9
β-strand	59-61	3	9
β-strand	69-74	6	8
β-strand	79-84	6	8
α-helix	89-91	3
β-strand	93-101	9	9
β-strand	106-108	3	9
β-strand	112-116	5	9

Chain H: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	14
α-helix	20	1
β-strand	21-28	8	14
β-strand	31-37	7	14
β-strand	46-47	2	14
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	14
β-strand	109-118	10	14
β-strand	121-126	6	14
β-strand	133-135	3	14
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
α-helix	183-185	3
β-strand	186-192	7	15
β-strand	198-208	11	15
β-strand	214-219	6	16
β-strand	222-223	2	16
β-strand	229-230	2	15
α-helix	231-233	3
β-strand	234-235	2	15
β-strand	241-250	10	15
β-strand	257-262	6	16
β-strand	270-272	3	16

Chain K: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	31
β-strand	12-14	3	32
β-strand	20-27	8	31
β-strand	33-41	9	32
β-strand	47-53	7	32
β-strand	59-61	3	32
β-strand	66	1	31
β-strand	69-74	6	31
β-strand	79-84	6	31
α-helix	89-91	3
β-strand	93-101	9	32
β-strand	106-108	3	32
β-strand	112-116	5	32

5 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A alpha chain	A, C, H, L	protein	279	Homo sapiens	A5I8L1 (AlphaFold model)
Beta-2-microglobulin	B, D, I, M	protein	99	Homo sapiens	P61769 (AlphaFold model)
Melanoma antigen recognized by T-cells 1	E, J, N, P	protein	10	Homo sapiens	Q16655 (AlphaFold model)
antibody AD01	F, G, K, O	protein	117	Homo sapiens
BXMart1-3 minibinder	Q, R, S, T	protein	102	synthetic construct

Sequence of entity 1 (A, C, H, L), FASTA

>9O5S_1 HLA class I histocompatibility antigen, A alpha chain (chains A, C, H, L)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEPSS

Sequence of entity 2 (B, D, I, M), FASTA

>9O5S_2 Beta-2-microglobulin (chains B, D, I, M)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (E, J, N, P), FASTA

>9O5S_3 Melanoma antigen recognized by T-cells 1 (chains E, J, N, P)
ELAGIGILTV

Sequence of entity 4 (F, G, K, O), FASTA

>9O5S_4 antibody AD01 (chains F, G, K, O)
EVKLVESGGGLVQPGGSLRLSCAASGSIFSINTMGWYRQTPGKQRDLVADISSGGSTKYG
DSVKGRFTISRDNTKNTVYLQMNSLKPEDTAVYYCYGLSYSNDDYWGQGTQVTVSSG

Sequence of entity 5 (Q, R, S, T), FASTA

>9O5S_5 BXMart1-3 minibinder (chains Q, R, S, T)
DPLKRLTELALEALRDEPHVPPEDRPLVTLLQIALNLAINVVVNRRHLGRTDPEHDRKLL
EELEEIRKLPREEAEKRLEELIERLEEENEKLAEEEVKQFRS

Primary citation

Design of high-specificity binders for peptide-MHC-I complexes. Liu, B., Greenwood, N.F., Bonzanini, J.E. et al. Science (2025) 389:386-391. DOI 10.1126/science.adv0185 · 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
9T2B 2.34 Å, Human Single Domain TCR-like Antibody 5F17 in complex with NY-ESO-1(C165V):HLA-A0201
9YTD 2.5 Å, Designed antibody vAB66 targeting PAP-HLA A*02:01
9T2C 2.89 Å, Human Single Domain TCR-like Antibody A10 in complex with NY-ESO-1(C165V):HLA-A0201

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