7K81: KIR3DL1*005

KIR3DL1*005 in complex with HLA-A*24:02 presenting the RYPLTFGW peptide. Determined by X-ray diffraction at 2.0 Å resolution. Released 9 Dec 2020.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 5,644
Mol. weight: 77.61 kDa
Ligands: NAG
Released: 9 Dec 2020

Explore 7K81 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7K81 contains 21 α-helices and 62 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-13	11	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-54	5
α-helix	57-84	28
β-strand	93-103	11	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	152-161	10
α-helix	163-174	12
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	223	1	4
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: 2 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
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: 9 helices, 32 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
α-helix	48	1
α-helix	49-52	4
α-helix	53-54	2
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
α-helix	186-191	6
β-strand	192-194	3	14
β-strand	195-197	3	13
α-helix	201-202	2
β-strand	204-207	4	15
β-strand	219-225	7	15
β-strand	231-236	6	16
β-strand	243-246	4	16
β-strand	248-249	2	15
β-strand	255-262	8	15
β-strand	268-275	8	16
β-strand	282-283	2	13
α-helix	284-289	6
β-strand	290-292	3	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	276	Homo sapiens	A0A5H2UYS3 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Arg-tyr-pro-leu-thr-phe-gly-trp	C	protein	8	synthetic construct	P04601 (AlphaFold model)
KIR3DL1	G	protein	289	Homo sapiens	P43629 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7K81_1 MHC class I antigen (chains A)
GSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETLQ
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>7K81_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>7K81_3 ARG-TYR-PRO-LEU-THR-PHE-GLY-TRP (chains C)
RYPLTFGW

Sequence of entity 4 (G), FASTA

>7K81_4 KIR3DL1 (chains G)
DKPFLSAWPSAVVPRGGHVTLRCHYRHRFNNFMLYKEDRIHIPIFHGRIFQESFNMSPVT
TAHAGNYTCRGSHPHSPTGWSAPSNPVVIMVTGNHRKPSLLAHPGPLVKSGERVILQCWS
DIMFEHFFLHKEGISKDPSRLVGQIHDGVSKANFSIGPMMLALAGTYRCYGSVTHTSYQL
SAPSDPLDIVVTGPYEKPSLSAQPGPKVQAGESVTLSCSSRSSYDMYHLSREGGAHERRL
PAVRKVNRTFQADFPLGPATHGGTYRCFGSFRHSPYELSDPSDPLLVSV

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

The Role of the HLA Class I alpha 2 Helix in Determining Ligand Hierarchy for the Killer Cell Ig-like Receptor 3DL1. Saunders, P.M., MacLachlan, B.J., Widjaja, J. et al. J Immunol (2021) 206:849-860. DOI 10.4049/jimmunol.2001109 · PubMed

Other PDB entries of the same protein (UniProt A0A5H2UYS3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7JYV 1.51 Å, Crystal Structure of HLA A*2402 in complex with YFSPIRVTF, an 9-mer influenza epitope
7MJA 1.69 Å, HLA-A*24:02 bound to Neuroblastoma derived PHOX2B peptide
7EJM 1.71 Å, Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-229E) spike protein
8SBK 1.8 Å, Structure of HLA-A*24:02 in complex with peptide, LYLPVRVLI (ATG2A).
7WT3 1.89 Å, Crystal structure of HLA-A*2402 complexed with 4-mer lipopeptide
7EJL 1.89 Å, Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-2) spike protein
7WT4 1.89 Å, Crystal structure of HLA-A*2402 complexed with 8-mer Influenza PB1 peptide
7EJN 2.11 Å, Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-HKU1) spike protein
6XQA 2.16 Å, Crystal Structure of HLA A*2402 in complex with TYQWVLKNL, an 9-mer epitope from…
7NME 2.2 Å, Human MHC Class I, A24 Allele presenting QLPRLFPLL, Complex with 4C6 TCR
7NMD 2.25 Å, Human Major Histocompatibility Complex A24 Allele presenting QLPRLFPLL
7K80 2.4 Å, KIR3DL1*001 in complex with HLA-A*24:02 presenting the RYPLTFGW peptide

Browse structure collections

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