SAXSdb — 3qt2

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

Interleukin-5 receptor subunit 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 20–335	Mutation：C66A, K72M, L138M, K167M, L234M	Interleukin-5 × 2 （P05113） BGC beta-D-glucopyranose × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；10% (w/v) PEG 20000, 0.1M MOPS pH 6.5, 20% (w/v) glucose, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.55 Å R-free 0.264
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 20–335	Mutation：C66A, K72M, L138M, K167M, L234M	Interleukin-5 × 2 （P05113） BGC beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；10% (w/v) PEG 20000, 0.1M MOPS pH 6.5, 20% (w/v) glucose, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.55 Å R-free 0.264

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 3QT2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OBX Crystal structure of the complex of PDZ2 of syntenin with an interleukin 5 receptor alpha peptide. Deposited 2003-01-31	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 B 413–420（8 aa） Fragment：LAST 8 RESIDUES, RESIDUES 413-420	Not recorded	CO COBALT (II) ION × 4 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；SITTING DROP 0.1 M HEPES, PH 7.0, 1.6 M AMMONIUM SULFATE, 20 MM COCL2, 0.2 M MGSO4 WITH MICROSEEDIN	Resolution 1.35 Å R-free 0.212
1OBZ Crystal structure of the complex of the PDZ tandem of syntenin with an interleukin 5 receptor alpha peptide. Deposited 2003-01-31	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 P 413–420（8 aa） Fragment：LAST 8 RESIDUES, RESIDUES 413-420	Not recorded	ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；SITTING DROP WITH 0.2 M SODIUM ACETATE, PH 4.6 28% PEG4000, 0.2 M AMMONIUM ACETATE	Resolution 1.70 Å R-free 0.213
3VA2 Crystal structure of human Interleukin-5 in complex with its alpha receptor Deposited 2011-12-28	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 C 21–335（315 aa） Fragment：ectodomain, UNP residues 21-335	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；0.1M Na HEPES, 22% (v/v) PEG 4000, 2% i-Propanol, 6% (w/v) 1,6-Hexanediol , pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.276
6H41 Structure of the complex of the IL-5 inhibitory peptide AF17121 bound to the IL-5 receptor IL-5Ralpha Deposited 2018-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 27–335（309 aa）	Mutation：C66A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；294 K；0.1 M sodium acetate pH 5.0, 3% (w/v) PEG 4000, 15% - 20% (v/v) 2-methyl-2,4-pentanediol	Resolution 2.75 Å R-free 0.226
8TLD Structure of the IL-5 Signaling Complex Deposited 2023-07-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 21–341（321 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

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

View Construct and Data Evidence

UniProt name	IL5RA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–317； UniProt 20–335 Author chain B； PDBConstruct 2–317； UniProt 20–335

Interleukin-5

Homo sapiens

UniProt P05113

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 C； UniProt 19–134 Chain D； UniProt 19–134	Not recorded	Interleukin-5 receptor subunit alpha × 1 （Q01344） BGC beta-D-glucopyranose × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；10% (w/v) PEG 20000, 0.1M MOPS pH 6.5, 20% (w/v) glucose, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.55 Å R-free 0.264
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 19–134 Chain F； UniProt 19–134	Not recorded	Interleukin-5 receptor subunit alpha × 1 （Q01344） BGC beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；10% (w/v) PEG 20000, 0.1M MOPS pH 6.5, 20% (w/v) glucose, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.55 Å R-free 0.264

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 3QT2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HUL A NOVEL DIMER CONFIGURATION REVEALED BY THE CRYSTAL STRUCTURE AT 2.4 ANGSTROMS RESOLUTION OF HUMAN INTERLEUKIN-5 Deposited 1995-03-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 24–131（108 aa） Chain B 24–131（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.369
3VA2 Crystal structure of human Interleukin-5 in complex with its alpha receptor Deposited 2011-12-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 23–134（112 aa） Fragment：UNP residues 23-134 Chain B 23–134（112 aa） Fragment：UNP residues 23-134	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；0.1M Na HEPES, 22% (v/v) PEG 4000, 2% i-Propanol, 6% (w/v) 1,6-Hexanediol , pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.276
8TLD Structure of the IL-5 Signaling Complex Deposited 2023-07-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 20–134（115 aa） Chain D 20–134（115 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9GVN DEPEMOKIMAB FAB IN COMPLEX WITH INTERLEUKIN 5 Deposited 2024-09-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 20–134（115 aa） Chain B 20–134（115 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Morpheus EDO_P8K, Morpheus Carboxylic acids, Morpheus buffer system 2	Resolution 1.93 Å R-free 0.209

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

View Construct and Data Evidence

UniProt name	IL5_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–117； UniProt 19–134 Author chain D； PDBConstruct 2–117； UniProt 19–134 Author chain E； PDBConstruct 2–117； UniProt 19–134 Author chain F； PDBConstruct 2–117； UniProt 19–134

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	3qt2
Deposition date deposition_date	2011-02-22
Structure title title	Structure of a cytokine ligand-receptor complex
Keywords keywords	;cytokine type I receptor fold, fibronectin type III modules, four-helical bundle, Cytokine, Ligand-receptor complex, membrane, PROTEIN BINDING-IMMUNE SYSTEM complex ;; PROTEIN BINDING/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	46.74 Å
Radius of gyration Rg (electron density) rg_electron	47.22 Å
Forward intensity I(0) i0	212384000.00
Molecular weight molecular_weight	121090.0 kDa
Excluded volume excluded_volume	152170 Å³
Envelope volume envelope_volume	225040 Å³
Hydration-shell volume shell_volume	42157 Å³
Envelope diameter envelope_diameter	170.9 Å
Shell Rg shell_rg	47.77 Å
Envelope Rg envelope_rg	46.20 Å
Shape Rg shape_rg	47.21 Å
Total Rg total_rg	47.25 Å
Total atoms total_atoms	8526
Residues n_residues	1051
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	169.9 Å
Rg (real space) rg_real	47.27 Å
Rg uncertainty (real space) rg_real_error	2.52 Å
I(0) (real space) i0_real	2.1240e+08
I(0) uncertainty (real space) i0_real_error	4.9660e+06
Rg (reciprocal space) rg_reciprocal	46.75 Å
I(0) (reciprocal space) i0_reciprocal	212200000.0000
Solution quality estimate total_estimate	0.7913
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	40.0 Å
Skewness Skewness skewness	0.450
Kurtosis Kurtosis kurtosis	-0.556
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12000000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.574; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.738; Smooth: 0.822

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Interleukin-5 receptor subunit alpha
Molecular weight formula_weight	36117.7 kDa
Mutation mutation	C66A, K72M, L138M, K167M, L234M
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8581

MADLLPDEKISLLPPVNFTIKVTGLAQVLLQWKPNPDQEQRNVNLEYQVKINAPKEDDYETRITESKAVTILHMGFSASVRTILQNDHSLLASSWASAELHAPPGSPGTSIVNLTCTTNTTEDNYSRLRSYQVSLHCTWMVGTDAPEDTQYFLYYRYGSWTEECQEYSMDTLGRNIACWFPRTFILSKGRDWLAVLVNGSSKHSAIRPFDQLFALHAIDQINPPLNVTAEIEGTRMSIQWEKPVSAFPIHCFDYEVKIHNTRNGYLQIEKLMTNAFISIIDDLSKYDVQVRAAVSSMCREAGLWSEWSQPIYVGFSR

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	Interleukin-5
Molecular weight formula_weight	13368.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MAIPTEIPTSALVKETLALLSTHRTLLIANETLRIPVPVHKNHQLCTEEIFQGIGTLESQTVQGGTVERLFKNLSLIKKYIDGQKKKCGEERRRVNQFLDYLQEFLGVMNTEWIIES

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 3 Entity 3 non-polymer

Description description	beta-D-glucopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	55

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3qt2c_
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.2 — Short-chain cytokines

Domain ID domain_id	d3qt2d_
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.2 — Short-chain cytokines

Domain ID domain_id	d3qt2e_
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.2 — Short-chain cytokines

Domain ID domain_id	d3qt2f_
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.2 — Short-chain cytokines

CATH v4.4 (10 domains)

Domain ID domain_id	3qt2A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3qt2A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3qt2A03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3qt2B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3qt2B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3qt2B03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3qt2C00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3qt2D00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3qt2E00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3qt2F00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	85.084 Å
Unit-cell length b length_b	61.633 Å
Unit-cell length c length_c	142.113 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.49 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	42.020 Å
R factor r_factor	0.2102
R_work r_work	0.2072
R_free r_free	0.2644

fit	/app/data/saxs_computation/qt/3qt2/3qt2.fit
pddf	/app/data/pr_computation/qt/3qt2/3qt2.pr.out
profile	/app/data/saxs_computation/qt/3qt2/3qt2.dat

Structure of a cytokine ligand-receptor complex

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

Interleukin-5 receptor subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Interleukin-5

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

CATH v4.4 (10 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)