4LL9: D3D4 domain of the LILRB1 molecule

Crystal structure of D3D4 domain of the LILRB1 molecule. Determined by X-ray diffraction at 2.69 Å resolution. Released 11 Sept 2013.

Method: X-ray diffraction
Resolution: 2.69 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,590
Mol. weight: 65.52 kDa
Released: 11 Sept 2013

Explore 4LL9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4LL9 contains 12 α-helices and 61 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: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	1
β-strand	15-16	2	2
β-strand	22-28	7	1
β-strand	34-39	6	3
β-strand	47-50	4	3
β-strand	58-64	7	1
α-helix	69-71	3
β-strand	73-80	8	3
β-strand	87	1	3
α-helix	89-93	5
β-strand	94-96	3	3
β-strand	97-98	2	2
β-strand	105	1	4
β-strand	107-109	3	5
β-strand	121-128	8	5
β-strand	134-140	7	6
β-strand	147-150	4	6
β-strand	152-153	2	5
β-strand	158-166	9	5
α-helix	169-171	3
β-strand	174-181	8	6
β-strand	184-188	5	6
α-helix	189	1
β-strand	190	1	4
α-helix	191-194	4
β-strand	195-196	2	6

Chain B: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	7
β-strand	15-16	2	8
β-strand	22-27	6	7
β-strand	34-39	6	9
β-strand	42-48	7	9
β-strand	59-64	6	7
α-helix	69-71	3
β-strand	73-80	8	9
α-helix	89-93	5
β-strand	94-96	3	9
β-strand	97-98	2	8
β-strand	107-109	3	10
β-strand	121-128	8	10
β-strand	134-139	6	11
β-strand	147-150	4	11
β-strand	152-153	2	10
β-strand	158-166	9	10
α-helix	169-171	3
β-strand	174-180	7	11
β-strand	181	1	12
β-strand	184	1	12
β-strand	187	1	8
α-helix	190-194	5
β-strand	195-196	2	11

Chain C: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	13
β-strand	15-16	2	14
β-strand	22-28	7	13
β-strand	34-39	6	15
β-strand	47-50	4	15
β-strand	58-64	7	13
α-helix	69-71	3
β-strand	73-80	8	15
α-helix	89-93	5
β-strand	94-96	3	15
β-strand	97-98	2	14
β-strand	106-109	4	16
β-strand	121-128	8	16
β-strand	134-139	6	17
β-strand	147-150	4	17
β-strand	152-153	2	16
β-strand	158-166	9	16
β-strand	174-180	7	17
β-strand	181	1	18
β-strand	184	1	18
β-strand	187	1	14
α-helix	189-194	6
β-strand	195-196	2	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leukocyte immunoglobulin-like receptor subfamily B member 1	A, B, C	protein	196	Homo sapiens	Q8NHL6 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>4LL9_1 Leukocyte immunoglobulin-like receptor subfamily B member 1 (chains A, B, C)
VSKKPSLSVQPGPIVAPEETLTLQCGSDAGYNRFVLYKDGERDFLQLAGAQPQAGLSQAN
FTLGPVSRSYGGQYRCYGAHNLSSEWSAPSDPLDILIAGQFYDRVSLSVQPGPTVASGEN
VTLLCQSQGWMQTFLLTKEGAADDPWRLRSTYQSQKYQAEFPMGPVTSAHAGTYRCYGSQ
SSKPYLLTHPSDPLEL

Primary citation

Crystal structures of the two membrane-proximal Ig-like domains (D3D4) of LILRB1/B2: alternative models for their involvement in peptide-HLA binding. Nam, G., Shi, Y., Ryu, M. et al. Protein Cell (2013) 4:761-770. DOI 10.1007/s13238-013-3908-x · PubMed

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)…
4NO0 2.7 Å, Crystal structure of non-phosphorylated form of RQA_V phosphopeptide bound to HLA-A2 in…
1VDG 2.8 Å, Crystal structure of LIR1.01, one of the alleles of LIR1
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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