9LLU: MHC class I antigen

p53 epitope specific TCR 4414A binding to p53Y220D-HLA-A2. Determined by X-ray diffraction at 2.87 Å resolution. Released 22 Jul 2026.

Method: X-ray diffraction
Resolution: 2.87 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,610
Mol. weight: 95.83 kDa
Released: 22 Jul 2026

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

Secondary structure: helices and β-sheets

9LLU contains 22 α-helices and 73 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, 23 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	94-98	5	1
β-strand	101-103	3	1
β-strand	109-112	4	1
β-strand	115-118	4	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	176-180	5
β-strand	183	1	2
β-strand	186-193	8	3
β-strand	199-206	8	3
β-strand	208	1	4
β-strand	209	1	2
β-strand	216-219	4	5
β-strand	222-223	2	5
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	4
β-strand	241-242	2	4
β-strand	245-249	5	3
β-strand	257-260	4	5
β-strand	271-272	2	5

Chain B: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	6
α-helix	4-5	2
β-strand	6-11	6	7
α-helix	14-15	2
β-strand	21-30	10	7
β-strand	31	1	6
β-strand	36-41	6	8
β-strand	44-45	2	8
α-helix	46	1
β-strand	50-51	2	7
α-helix	52-54	3
β-strand	55-56	2	7
β-strand	62-70	9	7
β-strand	78-83	6	8
β-strand	91-94	4	8

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3

Chain D: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	15
β-strand	19-24	6	16
β-strand	32-38	7	15
β-strand	45-51	7	15
β-strand	56-59	4	16
β-strand	62-67	6	16
α-helix	68-70	3
β-strand	72-77	6	16
α-helix	82-84	3
β-strand	86-94	9	15
β-strand	100-103	4	15
β-strand	107-111	5	15
β-strand	121-125	5	17
β-strand	135-139	5	17
α-helix	147-149	3
β-strand	156-157	2	17
α-helix	158-160	3
β-strand	161-165	5	17
β-strand	170-178	9	17
β-strand	198	1	17

Chain E: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	9
β-strand	10-14	5	10
β-strand	19-23	5	9
β-strand	31-37	7	10
α-helix	42-43	2
β-strand	44-50	7	10
β-strand	53-57	5	10
β-strand	64-68	5	9
β-strand	74-78	5	9
α-helix	83-85	3
β-strand	87-94	8	10
β-strand	111-116	6	10
β-strand	123	1	11
β-strand	126-130	5	12
α-helix	134-140	7
β-strand	142-152	11	12
β-strand	153	1	11
β-strand	157-163	7	13
β-strand	166	1	13
β-strand	172-174	3	12
β-strand	179-180	2	12
β-strand	190-199	10	12
α-helix	200-204	5
β-strand	209-216	8	13
β-strand	219	1	14
β-strand	233	1	14
β-strand	235-242	8	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	276	Homo sapiens	Q8WLS4 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Val-val-pro-asp-glu-pro-pro-glu-val	C	protein	9	Homo sapiens
T cell receptor 4414A chain beta	E	protein	247	Homo sapiens
T cell receptor 4414A chain alpha	D	protein	207	Homo sapiens

Sequence of entity 1 (A), FASTA

>9LLU_1 MHC class I antigen (chains A)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B), FASTA

>9LLU_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>9LLU_3 VAL-VAL-PRO-ASP-GLU-PRO-PRO-GLU-VAL (chains C)
VVPDEPPEV

Sequence of entity 4 (E), FASTA

>9LLU_4 T cell receptor 4414A chain beta (chains E)
METGVTQSPTHLIKTRGQQVTLRCSSQSGHNTVSWYQQALGQGPQFIFQYYREEENGRGN
FPPRFSGLQFPNYSSELNVNALELDDSALYLCASSLGGTGGIYNEQFFGPGTRLTVLEDL
KNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPL
KEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSA
EAWGRAD

Sequence of entity 5 (D), FASTA

>9LLU_5 T cell receptor 4414A chain alpha (chains D)
MGEDVEQSLFLSVREGDSSVINCTYTDSSSTYLYWYKQEPGAGLQLLTYIFSNMDMKQDQ
RLTVLLNKKDKHLSLRIADTQTGDSAIYFCAEISTSGTYKYIFGTGTRLKVLANIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Primary citation

Structural basis for T-cell receptor recognition of p53 Y220D , a human cancer neoantigen. Duan, Z., Zhao, J., Wu, J. et al. Acta Crystallogr D Struct Biol (2026) 82:1082-1092. DOI 10.1107/S2059798326007564 · PubMed

Other PDB entries of the same protein (UniProt Q8WLS4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9X7U 1.59 Å, Complex of HLA-A2, a class I MHC, with a UTP20 peptide
9WK0 1.8 Å, Neoantigen Rac1P29S-HLA-A2
21GJ 1.83 Å, Neoantigen p53Y220D-HLA-A2
21EX 2.02 Å, Wild tipe p53WT-HLA-A2
9XME 2.04 Å, Complex of HLA-A2, a class I MHC, with a wild type UTP20 peptide
9J4U 2.17 Å, Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by…
9PIX 2.35 Å, Mur14 Fab with HBV c18V pMHC
9PKC 2.5 Å, Mur35 Fab with HBV c18V pMHC
9PKF 2.6 Å, Mur35 Fab with HBV c18I pMHC
9PKV 2.72 Å, HU-38 Fab with PRAME pMHC
3HG1 3.0 Å, Germline-governed recognition of a cancer epitope by an immunodominant human T cell…
9C96 3.0 Å, Cryo-EM structure of TAP binding protein related (TAPBPR) in complex with HLA-A*02:01…

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