9SKP: HLA-A0201

Crystal structure of HLA-A0201 in complex with peptide SLLWNGPMAV. Determined by X-ray diffraction at 1.89 Å resolution. Released 17 Sept 2025.

Method: X-ray diffraction
Resolution: 1.89 Å
Organisms: Homo sapiens, Yellow fever virus
Chains: 3
Atoms: 3,497
Mol. weight: 46.03 kDa
Released: 17 Sept 2025

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

Secondary structure: helices and β-sheets

9SKP contains 14 α-helices and 30 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	19-20	2
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	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-224	3	4
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-273	4	4

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	276	Homo sapiens	A5I8L1 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
SLLWNGPMAV peptide	C	protein	10	Yellow fever virus	P03314 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9SKP_1 MHC class I antigen (chains A)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B), FASTA

>9SKP_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>9SKP_3 SLLWNGPMAV peptide (chains C)
SLLWNGPMAV

Primary citation

Key determinants of T cell epitope recognition revealed by TCR specificity profiles. Liu, Y., Croce, G., Tadros, D. et al. bioRxiv (2025). DOI 10.1101/2025.11.17.688817

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
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
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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