1VDG: LIR1.01, one of the alleles of LIR1

Crystal structure of LIR1.01, one of the alleles of LIR1. Determined by X-ray diffraction at 2.8 Å resolution. Released 2 Aug 2005.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,010
Mol. weight: 44 kDa
Released: 2 Aug 2005

Explore 1VDG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1VDG contains 13 α-helices and 37 β-strands across 2 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: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	7-11	5	1
β-strand	15-17	3	2
β-strand	22-27	6	1
β-strand	35-39	5	3
α-helix	47-49	3
α-helix	52-56	5
β-strand	59-62	4	1
α-helix	67-69	3
β-strand	71-77	7	3
α-helix	85-90	6
β-strand	91-93	3	3
β-strand	94-96	3	2
β-strand	103-107	5	4
β-strand	111-112	2	5
β-strand	118-123	6	4
β-strand	130-135	6	6
β-strand	144-147	4	6
β-strand	156-161	6	4
β-strand	171-177	7	6
β-strand	184-185	2	2
α-helix	187-191	5
β-strand	192-193	2	6
β-strand	195-196	2	5

Chain B: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	7-11	5	7
β-strand	15-17	3	8
β-strand	22-27	6	7
β-strand	35-39	5	9
α-helix	45-49	5
α-helix	52-55	4
β-strand	59-62	4	7
α-helix	67-69	3
β-strand	71-77	7	9
α-helix	85-90	6
β-strand	91-93	3	9
β-strand	94-96	3	8
α-helix	100-102	3
β-strand	103-107	5	10
β-strand	111-112	2	11
β-strand	118-123	6	10
β-strand	130-135	6	12
β-strand	144-147	4	12
β-strand	156-161	6	10
β-strand	171-177	7	12
β-strand	184	1	8
β-strand	185	1	12
α-helix	187-191	5
β-strand	192-193	2	12
β-strand	195-196	2	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leukocyte immunoglobulin-like receptor subfamily B member 1	A, B	protein	197	Homo sapiens	Q8NHL6 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1VDG_1 Leukocyte immunoglobulin-like receptor subfamily B member 1 (chains A, B)
GHLPKPTLWAEPGSVITQGSPVTLRCQGGQETQEYRLYREKKTALWITRIPQELVKKGQF
PIPSITWEHAGRYRCYYGSDTAGRSESSDPLELVVTGAYIKPTLSAQPSPVVNSGGNVIL
QCDSQVAFDGFSLCKEGEDEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYAYDSN
SPYEWSLPSDLLELLVL

Primary citation

Crystal structure of LIR1.03, one of the alleles of LIR1. Shiroishi, M., Rasubala, L., Kuroki, K. et al. To be published.

Other PDB entries of the same protein (UniProt Q8NHL6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1UGN 1.8 Å, Crystal structure of LIR1.02, one of the alleles of LIR1
1G0X 2.1 Å, Crystal structure of the ligand binding domain of lir-1 (ILT2)
3D2U 2.21 Å, Structure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a Host Inhibitory Receptor
6EWO 2.3 Å, Crystal structure of non-phosphorylated form of RTF PHOSPHOPEPTIDE BOUND TO HLA-A2 in…
6EWA 2.39 Å, Crystal structure of HLA-A2 in complex with LILRB1
7KFK 2.63 Å, Crystal structure of LILRB1 D3D4 domain in complex with Plasmodium RIFIN (PF3D7_1373400)…
4LL9 2.69 Å, Crystal structure of D3D4 domain of the LILRB1 molecule
4NO0 2.7 Å, Crystal structure of non-phosphorylated form of RQA_V phosphopeptide bound to HLA-A2 in…
1UFU 3.0 Å, Crystal structure of ligand binding domain of immunoglobulin-like transcript 2 (ILT2;…
6ZDX 3.0 Å, RIFIN variable region bound to LILRB1 ectodomain
6K60 3.15 Å, Structural and functional basis for HLA-G isoform recognition of immune checkpoint…
6EWC 3.2 Å, Crystal structure of non-phosphorylated form of RLS PHOSPHOPEPTIDE BOUND TO HLA-A2 in…

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