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1hul

A NOVEL DIMER CONFIGURATION REVEALED BY THE CRYSTAL STRUCTURE AT 2.4 ANGSTROMS RESOLUTION OF HUMAN INTERLEUKIN-5

Method: X-RAY DIFFRACTION Dmax: 68.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 24–131 Chain B； UniProt 24–131 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 Å R-free 0.369

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 1HUL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3QT2 Structure of a cytokine ligand-receptor complex Deposited 2011-02-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 19–134（116 aa）
Chain D 19–134（116 aa）
Not recorded 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
3QT2 Structure of a cytokine ligand-receptor complex Deposited 2011-02-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 19–134（116 aa）
Chain F 19–134（116 aa）
Not recorded 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
3VA2 Crystal structure of human Interleukin-5 in complex with its alpha receptor Deposited 2011-12-28 Different construct Different oligomeric state 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 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IL5_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–108； UniProt 24–131 Author chain B； PDBConstruct 1–108； UniProt 24–131

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1hul

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1hul
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1hul
Deposition date deposition_date1995-03-17
Structure title titleA NOVEL DIMER CONFIGURATION REVEALED BY THE CRYSTAL STRUCTURE AT 2.4 ANGSTROMS RESOLUTION OF HUMAN INTERLEUKIN-5
Keywords keywordsCYTOKINE; CYTOKINE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.72 Å
Radius of gyration Rg (electron density) rg_electron20.04 Å
Forward intensity I(0) i010497000.00
Molecular weight molecular_weight24763.0 kDa
Excluded volume excluded_volume31378 ų
Envelope volume envelope_volume36975 ų
Hydration-shell volume shell_volume16487 ų
Envelope diameter envelope_diameter67.9 Å
Shell Rg shell_rg24.94 Å
Envelope Rg envelope_rg20.10 Å
Shape Rg shape_rg20.02 Å
Total Rg total_rg20.86 Å
Total atoms total_atoms1742
Residues n_residues216
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax68.6 Å
Rg (real space) rg_real20.81 Å
Rg uncertainty (real space) rg_real_error0.62 Å
I(0) (real space) i0_real1.0500e+07
I(0) uncertainty (real space) i0_real_error1.5010e+05
Rg (reciprocal space) rg_reciprocal20.79 Å
I(0) (reciprocal space) i0_reciprocal10500000.0000
Solution quality estimate total_estimate0.7931
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.9 Å
Skewness Skewness skewness0.474
Kurtosis Kurtosis kurtosis-0.299
Angular range angular_range— – 0.3850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2350000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.788; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.944; Smooth: 0.000
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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1hula_
Class classa — All alpha proteins
Fold Fold folda.26 — 4-helical cytokines
Superfamily Superfamily superfamilya.26.1 — 4-helical cytokines
Family Family familya.26.1.2 — Short-chain cytokines
Domain ID domain_idd1hulb_
Class classa — All alpha proteins
Fold Fold folda.26 — 4-helical cytokines
Superfamily Superfamily superfamilya.26.1 — 4-helical cytokines
Family Family familya.26.1.2 — Short-chain cytokines

CATH v4.4 (2 domains)

Domain ID domain_id1hulA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1hulB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily10 —
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8. Citations (1)

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9. Files and Curves (10)