SAXSdb — 2gw5

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

Leukocyte immunoglobulin-like receptor subfamily B member 2 precursor

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 24–220	Fragment：N-terminal Domains 1 and 2	IPA ISOPROPYL ALCOHOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；0.1M Hepes pH 7.5, 10% Isopropanol, 20% PEG 4000 streak seeded., VAPOR DIFFUSION, HANGING DROP	Resolution 1.80 Å R-free 0.279

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 2GW5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2DYP Crystal Structure of LILRB2(LIR2/ILT4/CD85d) complexed with HLA-G Deposited 2006-09-15	Different construct 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 24–219（196 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M Tris-HCl pH8.0, 45% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.278
4LLA Crystal structure of D3D4 domain of the LILRB2 molecule Deposited 2013-07-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 222–419（198 aa）	Mutation：D3D4 domain, UNP residues 222-419	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；3.5M sodium formate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.50 Å R-free 0.272
4LLA Crystal structure of D3D4 domain of the LILRB2 molecule Deposited 2013-07-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 222–419（198 aa）	Mutation：D3D4 domain, UNP residues 222-419	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；3.5M sodium formate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.50 Å R-free 0.272
4LLA Crystal structure of D3D4 domain of the LILRB2 molecule Deposited 2013-07-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 222–419（198 aa）	Mutation：D3D4 domain, UNP residues 222-419	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；3.5M sodium formate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.50 Å R-free 0.272
6AED Crystal Structure of the four Ig-like domain of LILRB2(LIR2/ILT4/CD85d) Deposited 2018-08-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–419（393 aa） Fragment：UNP residues 27-419	Mutation：V213M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Tris, pH 8.5, 25%(v/v) tert-butanol	Resolution 3.80 Å R-free 0.287
9C9C Protein receptor Deposited 2024-06-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–220（199 aa） Fragment：residues 22-220 (Uniprot numbering)	Not recorded	CL CHLORIDE ION × 1 IMD IMIDAZOLE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；imidazole, peg	Resolution 1.66 Å R-free 0.196
9C9C Protein receptor Deposited 2024-06-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 22–220（199 aa） Fragment：residues 22-220 (Uniprot numbering)	Not recorded	CL CHLORIDE ION × 3 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；imidazole, peg	Resolution 1.66 Å R-free 0.196
9C9D Protein receptor Deposited 2024-06-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 22–220（199 aa） Fragment：residues 22-220 (Uniprot numbering)	Not recorded	30W N-(6-formyl-4-oxo-3,4-dihydropteridin-2-yl)acetamide × 1 GOL GLYCEROL × 3 SO4 SULFATE ION × 8 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；295 K；PEG 8K, (NH4)2SO4, MES	Resolution 2.90 Å R-free 0.215

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

View Construct and Data Evidence

UniProt name	LIRB2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–196； 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	2gw5
Deposition date deposition_date	2006-05-03
Structure title title	Crystal Structure of LIR-2 (ILT4) at 1.8 : differences from LIR-1 (ILT2) in regions implicated in the binding of the Cytomegalovirus class I MHC homolog UL18
Keywords keywords	Ig like domains, 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	20.27 Å
Radius of gyration Rg (electron density) rg_electron	19.47 Å
Forward intensity I(0) i0	7343740.00
Molecular weight molecular_weight	19875.0 kDa
Excluded volume excluded_volume	24803 Å³
Envelope volume envelope_volume	30158 Å³
Hydration-shell volume shell_volume	13779 Å³
Envelope diameter envelope_diameter	67.3 Å
Shell Rg shell_rg	24.56 Å
Envelope Rg envelope_rg	19.77 Å
Shape Rg shape_rg	19.48 Å
Total Rg total_rg	20.27 Å
Total atoms total_atoms	1402
Residues n_residues	184
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	67.3 Å
Rg (real space) rg_real	20.36 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	7.3440e+06
I(0) uncertainty (real space) i0_real_error	9.6620e+04
Rg (reciprocal space) rg_reciprocal	20.35 Å
I(0) (reciprocal space) i0_reciprocal	7344000.0000
Solution quality estimate total_estimate	0.7103
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.3 Å
Skewness Skewness skewness	0.384
Kurtosis Kurtosis kurtosis	-0.559
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2876000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 0.319; Positv: 1.000; Valcen: 0.821; Smooth: 0.960

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Leukocyte immunoglobulin-like receptor subfamily B member 2 precursor
Molecular weight formula_weight	21934.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1553

GTIPKPTLWAEPDSVITQGSPVTLSCQGSLEAQEYRLYREKKSASWITRIRPELVKNGQFHIPSITWEHTGRYGCQYYSRARWSELSDPLVLVMTGAYPKPTLSAQPSPVVTSGGRVTLQCESQVAFGGFILCKEGEDEHPQCLNSQPHARGSSRAIFSVGPVSPNRRWSHRCYGYDLNSPYVWSSPSDLLELLVPG

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	145

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2gw5a1
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.1.1.0 — automated matches

Domain ID domain_id	d2gw5a2
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 (2 domains)

Domain ID domain_id	2gw5A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2gw5A02
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	62.530 Å
Unit-cell length b length_b	62.530 Å
Unit-cell length c length_c	106.917 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	34.080 Å
R factor r_factor	0.2423
R_work r_work	0.2404
R_free r_free	0.2786

fit	/app/data/saxs_computation/gw/2gw5/2gw5.fit
pddf	/app/data/pr_computation/gw/2gw5/2gw5.pr.out
profile	/app/data/saxs_computation/gw/2gw5/2gw5.dat

Crystal Structure of LIR-2 (ILT4) at 1.8 : differences from LIR-1 (ILT2) in regions implicated in the binding of the Cytomegalovirus class I MHC homolog UL18

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

Leukocyte immunoglobulin-like receptor subfamily B member 2 precursor

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