SAXSdb — 1vdg

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Leukocyte immunoglobulin-like receptor subfamily B member 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 24–220 Chain B； UniProt 24–220	Fragment：Ligand binding domain (domain 1 and 2) Mutation：A70T	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.1M Tris chloride, 0.7M potassium sodium tartrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.301

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1VDG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1G0X CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN OF LIR-1 (ILT2) Deposited 2000-10-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–221（197 aa） Fragment：D1D2 LIGAND BINDING DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；potassium sodium tartarate, tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.244
1P7Q Crystal Structure of HLA-A2 Bound to LIR-1, a Host and Viral MHC Receptor Deposited 2003-05-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 25–221（197 aa） Fragment：residue 25-221	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 4000, Sodium Acetate, Tris, L-Cysteine, Triton X-100, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.40 Å R-free 0.309
1UFU Crystal structure of ligand binding domain of immunoglobulin-like transcript 2 (ILT2; LIR-1) Deposited 2003-06-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–221（197 aa） Fragment：Ligand binding domain (domain1 and 2)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；1.6M Sodium Formate, 0.08M Na-acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.00 Å R-free 0.300
1UGN Crystal structure of LIR1.02, one of the alleles of LIR1 Deposited 2003-06-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–221（198 aa） Fragment：Ligand binding domain (domain1 and 2)	Mutation：A70T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.1M Tris chloride, 0.7M potassium sodium tartrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.80 Å R-free 0.239
3D2U Structure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a Host Inhibitory Receptor Deposited 2008-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 24–221（198 aa） Fragment：Ig-like C2-type 1 and C2-type 2 domains	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 MAN alpha-D-mannopyranose × 1 BMA beta-D-mannopyranose × 1 FUC alpha-L-fucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.4 M Mg(NO3)2, and 16~22% (w/v) PEG 33500, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.21 Å R-free 0.259
3D2U Structure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a Host Inhibitory Receptor Deposited 2008-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 24–221（198 aa） Fragment：Ig-like C2-type 1 and C2-type 2 domains	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.4 M Mg(NO3)2, and 16~22% (w/v) PEG 33500, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.21 Å R-free 0.259
4LL9 Crystal structure of D3D4 domain of the LILRB1 molecule Deposited 2013-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 222–417（196 aa） Fragment：D3D4 domain, UNP residues 222-417	Not recorded	IOD IODIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；277 K；0.2M NaI, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.69 Å R-free 0.275
4LL9 Crystal structure of D3D4 domain of the LILRB1 molecule Deposited 2013-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 222–417（196 aa） Fragment：D3D4 domain, UNP residues 222-417	Not recorded	IOD IODIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；277 K；0.2M NaI, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.69 Å R-free 0.275
4LL9 Crystal structure of D3D4 domain of the LILRB1 molecule Deposited 2013-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 222–417（196 aa） Fragment：D3D4 domain, UNP residues 222-417	Not recorded	IOD IODIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；277 K；0.2M NaI, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.69 Å R-free 0.275
4NO0 Crystal structure of non-phosphorylated form of RQA_V phosphopeptide bound to HLA-A2 in complex with LILRB1 Deposited 2013-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 27–221（195 aa） Fragment：UNP residues 27-221	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；18% PEG3350, 0.1 M HEPES, pH 7.4, 0.2 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.309
5KNM Human leukocyte antigen F (HLA-F) presents peptides and regulates immunity through interactions with NK-cell receptors Deposited 2016-06-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 24–221（198 aa） Fragment：UNP residues 24-221	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；27% PEG 550 MME .1 M Tris-HCl 300 mM NaCl	Resolution 3.30 Å R-free 0.326

8 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LIRB1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–197； UniProt 24–220 Author chain B； PDBConstruct 1–197； UniProt 24–220

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1vdg
Deposition date deposition_date	2004-03-22
Structure title title	Crystal structure of LIR1.01, one of the alleles of LIR1
Keywords keywords	immunoglobulin-like, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	22.34 Å
Radius of gyration Rg (electron density) rg_electron	21.45 Å
Forward intensity I(0) i0	29588300.00
Molecular weight molecular_weight	41790.0 kDa
Excluded volume excluded_volume	52262 Å³
Envelope volume envelope_volume	63122 Å³
Hydration-shell volume shell_volume	24234 Å³
Envelope diameter envelope_diameter	70.2 Å
Shell Rg shell_rg	28.38 Å
Envelope Rg envelope_rg	21.27 Å
Shape Rg shape_rg	21.43 Å
Total Rg total_rg	22.37 Å
Total atoms total_atoms	2949
Residues n_residues	374
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	70.3 Å
Rg (real space) rg_real	22.22 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	2.9590e+07
I(0) uncertainty (real space) i0_real_error	3.7970e+05
Rg (reciprocal space) rg_reciprocal	22.25 Å
I(0) (reciprocal space) i0_reciprocal	29590000.0000
Solution quality estimate total_estimate	0.9040
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.9 Å
Skewness Skewness skewness	0.114
Kurtosis Kurtosis kurtosis	-0.540
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10130000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1vdga1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.4 — I set domains

Domain ID domain_id	d1vdga2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.4 — I set domains

Domain ID domain_id	d1vdgb1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.4 — I set domains

Domain ID domain_id	d1vdgb2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.4 — I set domains

CATH v4.4 (4 domains)

Domain ID domain_id	1vdgA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1vdgA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1vdgB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1vdgB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	40.969 Å
Unit-cell length b length_b	93.220 Å
Unit-cell length c length_c	57.773 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.82 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	19.980 Å
R factor r_factor	0.2500
R_work r_work	0.2410
R_free r_free	0.3010

Description description	Leukocyte immunoglobulin-like receptor subfamily B member 1
Molecular weight formula_weight	22000.7 kDa
Mutation mutation	A70T
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3010

Crystal structure of LIR1.01, one of the alleles of LIR1

1. Protein Identity and Related Structures Protein Identity & Related Structures

Leukocyte immunoglobulin-like receptor subfamily B member 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	61

fit	/app/data/saxs_computation/vd/1vdg/1vdg.fit
pddf	/app/data/pr_computation/vd/1vdg/1vdg.pr.out
profile	/app/data/saxs_computation/vd/1vdg/1vdg.dat