SAXSdb — 9pd2

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

Paired immunoglobulin-like type 2 receptor alpha

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 32–150	Not recorded	Anti-PILRA Fab Heavy Chain × 1 Anti-PILRA Fab Light Chain × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M CAPS pH 10.5, 20% PEG 8000, 0.2 M NaCl	Resolution 2.58 Å R-free 0.277

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 9PD2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4NFB Structure of paired immunoglobulin-like type 2 receptor (PILR ) Deposited 2013-10-31	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 32–150（119 aa） Fragment：UNP residues 32-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.1M sodium citrate tribasic dehydrate pH 5.6, 20%(v/v) 2-propanol, 20%(w/v) polyethylene glycol 4,000, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.225
5XO2 Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide II Deposited 2017-05-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 32–150（119 aa） Fragment：UNP residues 32-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M MES monohydrate pH 6.5, 1.6M Magnesium sulfate heptahydrate	Resolution 2.20 Å R-free 0.262
5XO2 Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide II Deposited 2017-05-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 32–150（119 aa） Fragment：UNP residues 32-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M MES monohydrate pH 6.5, 1.6M Magnesium sulfate heptahydrate	Resolution 2.20 Å R-free 0.262
5XOF Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide I Deposited 2017-05-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 32–150（119 aa） Fragment：UNP residues 32-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Tris-HCl pH8.5, 25% (w/v) PEG 6000	Resolution 1.96 Å R-free 0.269
5XOF Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide I Deposited 2017-05-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 32–150（119 aa） Fragment：UNP residues 32-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Tris-HCl pH8.5, 25% (w/v) PEG 6000	Resolution 1.96 Å R-free 0.269
5XOF Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide I Deposited 2017-05-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 32–150（119 aa） Fragment：UNP residues 32-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Tris-HCl pH8.5, 25% (w/v) PEG 6000	Resolution 1.96 Å R-free 0.269
5XOF Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide I Deposited 2017-05-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 32–150（119 aa） Fragment：UNP residues 32-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Tris-HCl pH8.5, 25% (w/v) PEG 6000	Resolution 1.96 Å R-free 0.269

3 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PILRA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 33–151； UniProt 32–150

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	9pd2
Deposition date deposition_date	2025-06-30
最后修订 last_revision	2025-12-17
Structure title title	Crystal structure of PILRA in complex with Fab portion of antagonist antibody
Keywords keywords	receptor, complex, fab, antibody, SIGNALING PROTEIN; SIGNALING PROTEIN
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	29.75 Å
Radius of gyration Rg (electron density) rg_electron	29.31 Å
Forward intensity I(0) i0	60485200.00
Molecular weight molecular_weight	61092.0 kDa
Excluded volume excluded_volume	76396 Å³
Envelope volume envelope_volume	97617 Å³
Hydration-shell volume shell_volume	29639 Å³
Envelope diameter envelope_diameter	104.6 Å
Shell Rg shell_rg	34.51 Å
Envelope Rg envelope_rg	29.10 Å
Shape Rg shape_rg	29.28 Å
Total Rg total_rg	29.90 Å
Total atoms total_atoms	4313
Residues n_residues	549
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	100.8 Å
Rg (real space) rg_real	29.93 Å
Rg uncertainty (real space) rg_real_error	1.17 Å
I(0) (real space) i0_real	6.0490e+07
I(0) uncertainty (real space) i0_real_error	1.0270e+06
Rg (reciprocal space) rg_reciprocal	29.86 Å
I(0) (reciprocal space) i0_reciprocal	60480000.0000
Solution quality estimate total_estimate	0.8633
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.4 Å
Skewness Skewness skewness	0.506
Kurtosis Kurtosis kurtosis	-0.288
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9084000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.808; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.881; Smooth: 0.921

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Paired immunoglobulin-like type 2 receptor alpha
Molecular weight formula_weight	17769.9 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	4370

MHHHHHHHHGLNDIFEAQKIEWHELEVLFQGPLYGVTQPKHLSASMGGSVEIPFSFYYPWELATAPDVRISWRRGHFHGQSFYSTRPPSIHKDYVNRLFLNWTEGQKSGFLRISNLQKQDQSVYFCRVELDTRSSGRQQWQSIEGTKLSIT

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 polymer

Description description	Anti-PILRA Fab Heavy Chain
Molecular weight formula_weight	23977.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVQLVQSGAEVKKPGASVKVSCKASGYTFTEYYMYWVRQAPGQGLELIGRIDPEDGGTDYIEKFKNRVTLTADTSTSTAYLELSSLRSEDTAVYYCATTIRGTVFAFWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

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	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	Anti-PILRA Fab Light Chain
Molecular weight formula_weight	23558.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIQMTQSPSSLSASVGDRVTITCRASEDIFNGLAWYQQKPGKSPKLLIYNAKTLHTGVPSRFSGSGSGSDYTLTISSLQPEDFATYFCQQYYDYPLTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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	Cricetulus griseus

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	27

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8. Citations (1)

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Unit-cell length a length_a	37.854 Å
Unit-cell length b length_b	46.753 Å
Unit-cell length c length_c	335.052 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.579 Å
Low-resolution limit resolution_low	46.347 Å
R factor r_factor	—
R_work r_work	0.2261
R_free r_free	0.2774

fit	/app/data/saxs_computation/pd/9pd2/9pd2.fit
pddf	/app/data/pr_computation/pd/9pd2/9pd2.pr.out
profile	/app/data/saxs_computation/pd/9pd2/9pd2.dat

Crystal structure of PILRA in complex with Fab portion of antagonist antibody

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

Paired immunoglobulin-like type 2 receptor alpha

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)