9LRF: Killer immunoglobulin receptor KIR2DL2

Killer immunoglobulin receptor KIR2DL2 in complex with KIR2DL2_KIR2DL2/3 agonist 61-Fab. Determined by X-ray diffraction at 2.5 Å resolution. Released 15 Oct 2025.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,674
Mol. weight: 70.81 kDa
Ligands: NAG
Released: 15 Oct 2025

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

Secondary structure: helices and β-sheets

9LRF contains 19 α-helices and 67 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 H: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-39	7	8
β-strand	45-51	7	8
β-strand	58-60	3	8
β-strand	65	1	7
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-101	10	8
β-strand	104	1	1
β-strand	107-113	7	8
β-strand	117-121	5	8
β-strand	127	1	9
β-strand	130-134	5	10
β-strand	146-155	10	10
β-strand	156	1	9
β-strand	161-164	4	11
α-helix	165-167	3
β-strand	173-175	3	10
α-helix	176-178	3
β-strand	179-180	2	10
β-strand	186-194	9	10
α-helix	196-198	3
β-strand	205-210	6	11
α-helix	211-213	3
β-strand	215-220	6	11

Chain K: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	30-34	5	1
β-strand	38-40	3	2
β-strand	45-51	7	1
β-strand	57-63	7	3
β-strand	68-73	6	3
β-strand	75-77	3	1
β-strand	80-87	8	1
α-helix	92-94	3
β-strand	96-103	8	3
α-helix	113-117	5
β-strand	118-120	3	3
β-strand	121-123	3	2
β-strand	130-134	5	4
β-strand	138-139	2	5
β-strand	144-151	8	4
β-strand	157-162	6	6
β-strand	168-171	4	6
α-helix	172	1
β-strand	173	1	4
β-strand	181-189	9	4
β-strand	195-201	7	6
β-strand	208	1	2
β-strand	209	1	6
α-helix	211-215	5
β-strand	216-217	2	6
β-strand	219-220	2	5

Chain L: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-13	4	13
β-strand	19-25	7	12
β-strand	33-38	6	13
α-helix	43-44	2
β-strand	45-49	5	13
β-strand	53-54	2	13
α-helix	55	1
β-strand	62-67	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	85-90	6	13
β-strand	97	1	8
β-strand	98	1	13
β-strand	102-106	5	13
α-helix	107-108	2
β-strand	109	1	14
α-helix	110-111	2
β-strand	112-116	5	15
α-helix	117-119	3
α-helix	120-124	5
β-strand	127-137	11	15
β-strand	138	1	14
β-strand	143-148	6	16
β-strand	151-152	2	16
β-strand	157-161	5	15
α-helix	162-165	4
β-strand	171-180	10	15
α-helix	181-186	6
β-strand	189-195	7	16
β-strand	203-208	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Killer cell immunoglobulin-like receptor 2DL2	K	protein	210	Homo sapiens	P43627 (AlphaFold model)
KIR2DL2_KIR2DL2/3 agonist 61 FAB FRAGMENT HEAVY CHAIN	H	protein	230	Homo sapiens
KIR2DL2_KIR2DL2/3 agonist 61 FAB FRAGMENT LIGHT CHAIN	L	protein	212	Homo sapiens

Sequence of entity 1 (K), FASTA

>9LRF_1 Killer cell immunoglobulin-like receptor 2DL2 (chains K)
HEGVHRKPSLLAHPGRLVKSEETVILQCWSDVRFEHFLLHREGKFKDTLHLIGEHHDGVS
KANFSIGPMMQDLAGTYRCYGSVTHSPYQLSAPSDPLDIVITGLYEKPSLSAQPGPTVLA
GESVTLSCSSRSSYDMYHLSREGEAHECRFSAGPKVNGTFQADFPLGPATHGGTYRCFGS
FRDSPYEWSNSSDPLLVSVIGNPSHHHHHH

Sequence of entity 2 (H), FASTA

>9LRF_2 KIR2DL2_KIR2DL2/3 agonist 61 FAB FRAGMENT HEAVY CHAIN (chains H)
QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSFAISWVRQAPGQGLEWMGGIIPIFGTANY
AQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARVSGTTGGYYYGMDVWGQGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 3 (L), FASTA

>9LRF_3 KIR2DL2_KIR2DL2/3 agonist 61 FAB FRAGMENT LIGHT CHAIN (chains L)
AIRMTQSPSSVSASVGDRVTITCRASQGIGNWLAWYQQKPGRAPKLLISTASSLQSGVPS
RFSGGGSGRGFTLTISSLQLEDFATYYCQQSYITPWTFGQGTKVEIKVAAPSVFIFPPSD
EQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLS
KADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Selective agonists of KIR and NKG2A to evade missing self response of natural killer cells. Hiura, S., Kuwasaki, Y., Nishikawa, Y. et al. Sci Rep (2025) 15:33550-33550. DOI 10.1038/s41598-025-18394-z · PubMed

Other PDB entries of the same protein (UniProt P43627 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9L4I 2.5 Å, Crystal structure of HLA-C*14:02 complexed with KIR2DL2
9LRA 2.6 Å, Killer immunoglobulin receptor KIR2DL2 in complex with Pan2D Fab
2DLI 2.9 Å, Killer immunoglobulin receptor 2DL2,TRIGONAL form
8TMU 2.9 Å, HLA-B*73:01 bound to a 10mer peptide in complex with KIR2DL2
1EFX 3.0 Å, Structure of a complex between the human natural killer cell receptor KIR2DL2 and a…
2DL2 3.0 Å, Killer immunoglobulin receptor 2DL2
6PA1 3.01 Å, Killer cell immunoglobulin-like receptor 2DL2 in complex with HLA-C*07:02
9L4H 3.1 Å, Crystal structure of HLA-C*14:03 complexed with KIR2DL2
9LRH 3.4 Å, Killer immunoglobulin receptor KIR2DL2 in complex with KIR2DL2_KIR2DL2/3 agonist 61-scFv

Browse structure collections

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