9D96: KIR3DL - HLA complex

KIR3DL - HLA complex. Determined by X-ray diffraction at 2.4 Å resolution. Released 3 Sept 2025.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Homo sapiens, human gammaherpesvirus 4
Chains: 4
Atoms: 5,500
Mol. weight: 78.97 kDa
Ligands: NAG
Released: 3 Sept 2025

Explore 9D96 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D96 contains 23 α-helices and 64 β-strands across 4 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: 12 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	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	152-158	7
α-helix	159-164	6
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	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	270-272	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	35-41	7	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	78-84	7	7
β-strand	91-94	4	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3

Chain G: 7 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	8
β-strand	17-19	3	9
β-strand	24-29	6	8
β-strand	34	1	8
β-strand	37-41	5	10
β-strand	44	1	10
α-helix	50-52	3
β-strand	55	1	10
β-strand	58-61	4	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	142-143	2
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
β-strand	185	1	14
α-helix	187-191	5
β-strand	192-194	3	14
β-strand	195-197	3	13
α-helix	201-202	2
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	248-251	4	15
β-strand	254-260	7	15
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)
Epstein-Barr nuclear antigen 2	C	protein	10	human gammaherpesvirus 4	P12978 (AlphaFold model)
Killer cell immunoglobulin-like receptor 3DL1	G	protein	301	Homo sapiens	P43629 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9D96_1 MHC class I antigen (chains A)
GSHSMRYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYW
DRNTQICKTNTQTYRENLRIALRYYNQSEAGSHTLQRMYGCDVGPDGRLLRGHNQFAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRTYLEGTCVEWLRRYLENGKETLQ
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>9D96_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>9D96_3 Epstein-Barr nuclear antigen 2 (chains C)
YHLIVDTDSL

Sequence of entity 4 (G), FASTA

>9D96_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 viral antigen. Zhu, D., 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:

9D97 1.6 Å, KIR3DL - HLA complex
9D95 2.8 Å, TCR - peptide - HLA complex

Browse structure collections

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