SAXSdb — 8y31

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

Interferon alpha/beta receptor 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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 1–333	Not recorded	QX006N-Fab-LC × 1 QX006N-Fab-HC × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION, RECRYSTALLIZATION；289 K；8%(w/v) PEG3350 50 mM Na-Citrate pH 5.5, 100 mM (NH4)2Citrate, 250 mM NaCl, 5 mM Hexadecyltrimethylammonium Bromide	Resolution 2.68 Å R-free 0.239
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 1–333	Not recorded	QX006N-Fab-LC × 1 QX006N-Fab-HC × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION, RECRYSTALLIZATION；289 K；8%(w/v) PEG3350 50 mM Na-Citrate pH 5.5, 100 mM (NH4)2Citrate, 250 mM NaCl, 5 mM Hexadecyltrimethylammonium Bromide	Resolution 2.68 Å R-free 0.239

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 8Y31	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3S98 human IFNAR1 Deposited 2011-06-01	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 30–332（303 aa） Fragment：UNP Residues 30-332	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions 298 K；20% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.234
3SE3 human IFNa2-IFNAR ternary complex Deposited 2011-06-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 28–436（409 aa） Fragment：IFNa2(YNS) (UNP Residues 28-436)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；293 K；15% (w/v) PEG 3350, 100 mM Na malonate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 4.00 Å R-free 0.311
3SE4 human IFNw-IFNAR ternary complex Deposited 2011-06-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 28–436（409 aa） Fragment：IFNw (UNP Residues 28-436)	Mutation：N101Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；293 K；19% (w/v) PEG 3350, 100 mM Ammonium sulfate, 100 mM Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.50 Å R-free 0.288
4PO6 Crystal structure of the human TYK2 FERM and SH2 domains with an IFNAR1 intracellular peptide Deposited 2014-02-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 478–507（30 aa） Fragment：unp residues 475-507	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；293 K；0.1 M Tris HCl pH 7.0, 0.2 M MgCl2, and 8-12% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.99 Å R-free 0.234

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	INAR1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–333； UniProt 1–333 Author chain F； PDBConstruct 1–333； UniProt 1–333

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	8y31
Deposition date deposition_date	2024-01-28
最后修订 last_revision	2024-12-04
Structure title title	The crystal structure of the QX006N-Fab/IFNAR1-SD123 complex
Keywords keywords	IFNAR1, QX006N, the QX006N-Fab-IFNAR1-SD123 complex, 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	34.44 Å
Radius of gyration Rg (electron density) rg_electron	33.72 Å
Forward intensity I(0) i0	215418000.00
Molecular weight molecular_weight	117250.0 kDa
Excluded volume excluded_volume	146460 Å³
Envelope volume envelope_volume	196390 Å³
Hydration-shell volume shell_volume	48168 Å³
Envelope diameter envelope_diameter	114.6 Å
Shell Rg shell_rg	40.98 Å
Envelope Rg envelope_rg	33.11 Å
Shape Rg shape_rg	33.71 Å
Total Rg total_rg	34.32 Å
Total atoms total_atoms	8262
Residues n_residues	1076
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	110.5 Å
Rg (real space) rg_real	34.34 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	2.1540e+08
I(0) uncertainty (real space) i0_real_error	3.2450e+06
Rg (reciprocal space) rg_reciprocal	34.41 Å
I(0) (reciprocal space) i0_reciprocal	215400000.0000
Solution quality estimate total_estimate	0.6720
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	43.2 Å
Skewness Skewness skewness	0.235
Kurtosis Kurtosis kurtosis	-0.398
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	26430000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 0.038; Positv: 1.000; Valcen: 0.995; Smooth: 0.897

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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	QX006N-Fab-LC
Molecular weight formula_weight	23200.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	8330

AIQMTQSPSSLSASVGDRVTITCQASQSISNQLSWYQQKPGKAPKLLIYDASSLASGVPSRFSGSRSGTKFTLTISSLQPEDFATYYCLGIYGDGADDGIAFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTQGTTSVTKSFNRGEC

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	QX006N-Fab-HC
Molecular weight formula_weight	24517.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

EVQLVESGGGLVQPGGSLRLSCAASGFSLSSYYMTWVRQAPGKGLEWVSVINVYGGTYYASWAKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAREDVAVYMAIDLWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGGHHHHHH

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	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Interferon alpha/beta receptor 1
Molecular weight formula_weight	39767.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

MMVVLLGATTLVLVAVAPWVLSAAAGGKNLKSPQKVEVDIIDDNFILRWNRSDESVGNVTFSFDYQKTGMDNWIKLSGCQNITSTKCNFSSLKLNVYEEIKLRIRAEKENTSSWYEVDSFTPFRKAQIGPPEVHLEAEDKAIVIHISPGTKDSVMWALDGLSFTYSLVIWKNSSGVEERIENIYSRHKIYKLSPETTYCLKVKAALLTSWKIGVYSPVHCIKTTVENELPPPENIEVSVQNQNYVLKWDYTYANMTFQVQWLHAFLKRNPGNHLYKWKQIPDCENVKTTQCVFPQNVFQKGIYLLRVQASDGNNTSFWSEEIKFDTEIQAFLLEVLFQGPHHHHHH

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	Homo sapiens

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	68

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8. Citations (1)

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Unit-cell length a length_a	73.155 Å
Unit-cell length b length_b	121.031 Å
Unit-cell length c length_c	79.738 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.51 °
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	2.680 Å
Low-resolution limit resolution_low	46.890 Å
R factor r_factor	0.1965
R_work r_work	0.1944
R_free r_free	0.2392

fit	/app/data/saxs_computation/y3/8y31/8y31.fit
pddf	/app/data/pr_computation/y3/8y31/8y31.pr.out
profile	/app/data/saxs_computation/y3/8y31/8y31.dat

The crystal structure of the QX006N-Fab/IFNAR1-SD123 complex

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

Interferon alpha/beta receptor 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 (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)