6L9N: H2-Ld

H2-Ld complexed with A5 peptide. Determined by X-ray diffraction at 2.6 Å resolution. Released 18 Nov 2020.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 12
Atoms: 12,879
Mol. weight: 179.73 kDa
Released: 18 Nov 2020

Explore 6L9N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6L9N contains 43 α-helices and 122 β-strands across 8 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.

Chains A, D and G: 10 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	45-47	3	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	159-164	6
α-helix	165-179	15
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-195	10	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	229-230	2	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	270-272	3	4

Chains B and H: 1 helix, 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	36-41	6	7
β-strand	44-45	2	7
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 E: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	4-5	2
β-strand	6-11	6	13
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	36-41	6	14
β-strand	44-45	2	14
β-strand	50-51	2	13
β-strand	55-56	2	13
β-strand	62-70	9	13
β-strand	78-83	6	14
β-strand	91-94	4	14

Chain J: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	22
α-helix	20	1
β-strand	21-28	8	22
β-strand	31-37	7	22
β-strand	45-47	3	22
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	22
β-strand	109-118	10	22
β-strand	121-126	6	22
β-strand	133-135	3	22
α-helix	138-150	13
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-179	15
β-strand	183	1	23
α-helix	184-185	2
β-strand	186-195	10	24
β-strand	198-208	11	24
β-strand	209	1	23
β-strand	214-216	3	25
β-strand	217-219	3	26
β-strand	222-224	3	26
β-strand	229-230	2	24
α-helix	231-233	3
β-strand	234-235	2	24
β-strand	241-250	10	24
α-helix	254-256	3
β-strand	257	1	26
β-strand	259-262	4	25
β-strand	270-272	3	25

Chain K: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	27
β-strand	6-11	6	28
β-strand	21-30	10	28
β-strand	31	1	27
β-strand	36-41	6	29
β-strand	44-45	2	29
β-strand	50-51	2	28
β-strand	55-56	2	28
β-strand	62-70	9	28
β-strand	78-83	6	29
β-strand	91-94	4	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC	A, D, G, J	protein	278	Homo sapiens	P01897 (AlphaFold model)
b2m	B, E, H, K	protein	99	Homo sapiens	P01887 (AlphaFold model)
Ser-pro-ser-tyr-ala-tyr-his-gln-phe	C, F, I, L	protein	9	Homo sapiens

Sequence of entity 1 (A, D, G, J), FASTA

>6L9N_1 MHC (chains A, D, G, J)
AGPHSMRYFETAVSRPGLGEPRYISVGYVDNKEFVRFDSDAENPRYEPQAPWMEQEGPEY
WERITQIAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQWMYGCDVGSDGRLLRGYEQFAYD
GCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNGNATL
LRTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDG
TFQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEPP

Sequence of entity 2 (B, E, H, K), FASTA

>6L9N_2 b2m (chains B, E, H, K)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (C, F, I, L), FASTA

>6L9N_3 SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE (chains C, F, I, L)
SPSYAYHQF

Primary citation

Structures suggest an approach for converting weak self-peptide tumor antigens into superagonists for CD8 T cells in cancer. Wei, P., Jordan, K.R., Buhrman, J.D. et al. Proc Natl Acad Sci U S A (2021) 118. DOI 10.1073/pnas.2100588118 · PubMed

Other PDB entries of the same protein (UniProt P01897 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3V4U 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UO1 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3V52 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UYR 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
6L9K 1.8 Å, H2-Ld a1a2 complexed with A5 peptide
8D5N 1.8 Å, Crystal structure of Ld-HF10
3VJ6 1.9 Å, Structure of the MHC class Ib molecule Qa-1b
4MS8 1.92 Å, 42F3 TCR pCPB9/H-2Ld Complex
3ERY 1.95 Å, Different thermodynamic binding mechanisms and peptide fine specificities associated…
5VCL 2.05 Å, Structure of the Qdm peptide bound to Qa-1a
3TJH 2.12 Å, 42F3-p3A1/H2-Ld complex
2OI9 2.35 Å, Structure of the 2C/Ld/QL9 allogeneic complex

Browse structure collections

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