9D97: KIR3DL - HLA complex

KIR3DL - HLA complex. Determined by X-ray diffraction at 1.6 Å resolution. Released 3 Sept 2025.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,961
Mol. weight: 78.99 kDa
Ligands: NAG
Released: 3 Sept 2025

Explore 9D97 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D97 contains 23 α-helices and 62 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: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	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	57-85	29
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	152-159	8
α-helix	160-164	5
α-helix	165-174	10
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	222-223	2	4
α-helix	225-227	3
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

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 G: 9 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	8
β-strand	17-19	3	9
β-strand	24-30	7	8
β-strand	33-34	2	8
β-strand	37-41	5	10
α-helix	50-52	3
β-strand	55	1	10
β-strand	59-61	3	8
α-helix	66-68	3
β-strand	70-76	7	10
β-strand	77	1	11
β-strand	85	1	11
β-strand	92-94	3	10
β-strand	95-97	3	9
β-strand	104-108	5	12
β-strand	112-114	3	13
β-strand	119-125	7	12
β-strand	131-136	6	14
α-helix	141-143	3
β-strand	144-147	4	14
β-strand	149-151	3	12
β-strand	154-161	8	12
α-helix	166-168	3
β-strand	170-177	8	14
β-strand	184	1	9
α-helix	185-191	7
β-strand	192-194	3	14
β-strand	195-197	3	13
α-helix	201-203	3
β-strand	204-208	5	15
β-strand	220-225	6	15
β-strand	231-236	6	13
β-strand	242-246	5	13
β-strand	248	1	15
β-strand	255-260	6	15
α-helix	261	1
α-helix	266-267	2
β-strand	268-275	8	13
β-strand	282-283	2	13
α-helix	284-289	6
β-strand	290-292	3	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	276	Homo sapiens	E5FQ58 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Cyclin-A2	C	protein	9	Homo sapiens	P20248 (AlphaFold model)
Killer cell immunoglobulin-like receptor 3DL1	G	protein	301	Homo sapiens	P43629 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9D97_1 MHC class I antigen (chains A)
GSHSMRYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYW
DRNTQICKTNTQTYRENLRIALRYYNQSEAGSHTLQRMYGCDVGPDGRLLRGHNQFAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRTYLEGTCVEWLRRYLENGKETLQ
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>9D97_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>9D97_3 Cyclin-A2 (chains C)
YHEDIHTYL

Sequence of entity 4 (G), FASTA

>9D97_4 Killer cell immunoglobulin-like receptor 3DL1 (chains G)
GSHMGGQDKPFLSAWPSAVVPRGGHVTLRCHYRHRFNNFMLYKEDRIHIPIFHGRIFQES
FNMSPVTTAHAGNYTCRGSHPHSPTGWSAPSNPVVIMVTGNHRKPSLLAHPGPLVKSGER
VILQCWSDIMFEHFFLHKEGISKDPSRLVGQIHDGVSKANFSIGPMMLALAGTYRCYGSV
THTPYQLSAPSDPLDIVVTGPYEKPSLSAQPGPKVQAGESVTLSCSSRSSYDMYHLSREG
GAHERRLPAVRKVNRTFQADFPLGPATHGGTYRCFGSFRHSPYEWSDPSDPLLVSVTGNP
S

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

KIR3D recognition of a self-epitope. Zhu, S., Petersen, J., Rossjohn, J. To be published.

Other PDB entries of the same protein (UniProt E5FQ58 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9D96 2.4 Å, KIR3DL - HLA complex
9D95 2.8 Å, TCR - peptide - HLA complex

Browse structure collections

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