6PA1: Killer cell immunoglobulin-like receptor 2DL2

Killer cell immunoglobulin-like receptor 2DL2 in complex with HLA-C*07:02. Determined by X-ray diffraction at 3.01 Å resolution. Released 16 Dec 2020.

Method: X-ray diffraction
Resolution: 3.01 Å
Organisms: Homo sapiens, synthetic construct
Chains: 8
Atoms: 9,106
Mol. weight: 134.21 kDa
Released: 16 Dec 2020

Explore 6PA1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PA1 contains 26 α-helices and 97 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.

Chain A: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	1
α-helix	14	1
α-helix	19-20	2
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	45-47	3	1
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	139-150	12
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
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	213-218	6	4
β-strand	223	1	4
β-strand	234-235	2	3
β-strand	241-250	10	3
β-strand	258-263	6	4
α-helix	269	1
β-strand	270-272	3	4

Chain B: 0 helices, 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
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chains C and G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4

Chain D: 3 helices, 19 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	36-42	7	10
β-strand	47-52	6	10
β-strand	54-55	2	8
β-strand	60-66	7	8
α-helix	71-73	3
β-strand	75-82	8	10
α-helix	92-96	5
β-strand	97-99	3	10
β-strand	100-102	3	9
β-strand	109-113	5	11
β-strand	125-130	6	11
β-strand	136-141	6	12
β-strand	148-151	4	12
β-strand	153	1	11
β-strand	160-165	6	11
β-strand	173-181	9	12
β-strand	184-188	5	12
α-helix	190-192	3
β-strand	195-197	3	12

Chain E: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	13
α-helix	14	1
α-helix	19-20	2
β-strand	21-28	8	13
β-strand	31-37	7	13
β-strand	45-47	3	13
α-helix	57-84	28
β-strand	93-103	11	13
β-strand	109-118	10	13
β-strand	121-126	6	13
β-strand	133-135	3	13
α-helix	139-150	12
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
β-strand	183	1	14
α-helix	184-185	2
β-strand	186-193	8	15
β-strand	198-208	11	15
β-strand	209	1	14
β-strand	213-218	6	16
β-strand	223	1	16
β-strand	233-235	3	15
β-strand	241-250	10	15
β-strand	258-263	6	16
α-helix	269	1
β-strand	270-272	3	16

Chain F: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	17
β-strand	6-11	6	18
β-strand	21-30	10	18
β-strand	31	1	17
β-strand	35-41	7	19
β-strand	44-45	2	19
β-strand	50-51	2	18
β-strand	55-56	2	18
β-strand	62-70	9	18
β-strand	78-84	7	19
β-strand	91-94	4	19

Chain H: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	20
β-strand	17-19	3	21
β-strand	24-30	7	20
β-strand	36-42	7	22
β-strand	47-52	6	22
β-strand	54	1	20
β-strand	60-66	7	20
α-helix	71-73	3
β-strand	75-82	8	22
α-helix	92-96	5
β-strand	97-99	3	22
β-strand	100-102	3	21
β-strand	109-113	5	23
β-strand	125-130	6	23
β-strand	136-140	5	24
β-strand	149-151	3	24
β-strand	153	1	23
β-strand	160-165	6	23
β-strand	173-175	3	25
β-strand	176-181	6	24
β-strand	184-188	5	24
α-helix	190-192	3
β-strand	195-197	3	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, Cw-7 alpha chain	A, E	protein	277	Homo sapiens	P10321 (AlphaFold model)
Beta-2-microglobulin	B, F	protein	100	Homo sapiens	P61769 (AlphaFold model)
Arg-tyr-arg-pro-gly-thr-val-ala-leu	C, G	protein	9	synthetic construct	P68431 (AlphaFold model)
Killer cell immunoglobulin-like receptor 2DL2	D, H	protein	204	Homo sapiens	P43627 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>6PA1_1 HLA class I histocompatibility antigen, Cw-7 alpha chain (chains A, E)
CSHSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYW
DRETQKYKRQAQADRVSLRNLRGYYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDG
KDYIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQ
RAEPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPS

Sequence of entity 2 (B, F), FASTA

>6PA1_2 Beta-2-microglobulin (chains B, F)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, G), FASTA

>6PA1_3 ARG-TYR-ARG-PRO-GLY-THR-VAL-ALA-LEU (chains C, G)
RYRPGTVAL

Sequence of entity 4 (D, H), FASTA

>6PA1_4 Killer cell immunoglobulin-like receptor 2DL2 (chains D, H)
HEGVHRKPSLLAHPGRLVKSEETVILQCWSDVRFEHFLLHREGKFKDTLHLIGEHHDGVS
KANFSIGPMMQDLAGTYRCYGSVTHSPYQLSAPSDPLDIVITGLYEKPSLSAQPGPTVLA
GESVTLSCSSRSSYDMYHLSREGEAHECRFSAGPKVNGTFQADFPLGPATHGGTYRCFGS
FRDSPYEWSNSSDPLLVSVIGNPS

Primary citation

Structural plasticity of KIR2DL2 and KIR2DL3 enables altered docking geometries atop HLA-C. Moradi, S., Stankovic, S., O'Connor, G.M. et al. Nat Commun (2021) 12:2173-2173. DOI 10.1038/s41467-021-22359-x · PubMed

Other PDB entries of the same protein (UniProt P10321 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6JTO 1.7 Å, Crystal structure of HLA-C05 in complex with a tumor mut10m peptide
5W6A 1.74 Å, HLA-C*06:02 presenting ARTELYRSL
4NT6 1.84 Å, HLA-C*0801 Crystal Structure
5W67 2.3 Å, HLA-C*06:02 presenting VRSRR(ABA)LRL
5VGD 2.32 Å, Crystal Structure of HLA-C*0501 in complex with SAE
3BZF 2.5 Å, The human non-classical major histocompatibility complex molecule HLA-E
6PAG 2.5 Å, Killer cell immunoglobulin-like receptor 2DL3 in complex with HLA-C*07:02
5VGE 2.6 Å, Crystal structure of HLA-C*07:02 in complex with RYR peptide
1QQD 2.7 Å, Crystal structure of HLA-CW4, a ligand for the KIR2D natural killer cell inhibitory…
1IM9 2.8 Å, Crystal structure of the human natural killer cell inhibitory receptor KIR2DL1 bound to…
5W69 2.8 Å, HLA-C*06:02 presenting ARFNDLRFV
1EFX 3.0 Å, Structure of a complex between the human natural killer cell receptor KIR2DL2 and a…

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