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6h41

Structure of the complex of the IL-5 inhibitory peptide AF17121 bound to the IL-5 receptor IL-5Ralpha

Method: X-RAY DIFFRACTION Dmax: 96.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Interleukin-5 receptor subunit alpha

Homo sapiens

UniProt Q01344

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 27–335 Mutation：C66A VAL-ASP-GLU-CYS-TRP-ARG-ILE-ILE-ALA-SER-HIS-THR-TRP-PHE-CYS-ALA-GLU-GLU × 1 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

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 6H41 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 oligomeric state 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
3QT2 Structure of a cytokine ligand-receptor complex Deposited 2011-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 20–335（316 aa）
Mutation：C66A, K72M, L138M, K167M, L234M 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 20–335（316 aa）
Mutation：C66A, K72M, L138M, K167M, L234M 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 mutation/modification Different oligomeric state 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
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 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IL5RA_HUMAN
Isoform Q01344-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–309； UniProt 27–335

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 6h41

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6h41
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6h41
Deposition date deposition_date2018-07-20
Structure title titleStructure of the complex of the IL-5 inhibitory peptide AF17121 bound to the IL-5 receptor IL-5Ralpha
Keywords keywordsInterleukin-5, inhibitor peptide, peptide-receptor complex, atopic diseases, CYTOKINE; 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_guinier27.22 Å
Radius of gyration Rg (electron density) rg_electron26.86 Å
Forward intensity I(0) i023713700.00
Molecular weight molecular_weight37344.0 kDa
Excluded volume excluded_volume46721 ų
Envelope volume envelope_volume60998 ų
Hydration-shell volume shell_volume20734 ų
Envelope diameter envelope_diameter99.0 Å
Shell Rg shell_rg30.90 Å
Envelope Rg envelope_rg27.46 Å
Shape Rg shape_rg26.84 Å
Total Rg total_rg27.40 Å
Total atoms total_atoms2637
Residues n_residues327
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 dmax96.7 Å
Rg (real space) rg_real27.43 Å
Rg uncertainty (real space) rg_real_error1.01 Å
I(0) (real space) i0_real2.3710e+07
I(0) uncertainty (real space) i0_real_error3.9990e+05
Rg (reciprocal space) rg_reciprocal27.37 Å
I(0) (reciprocal space) i0_reciprocal23710000.0000
Solution quality estimate total_estimate0.8376
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.4 Å
Skewness Skewness skewness0.443
Kurtosis Kurtosis kurtosis-0.357
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4467000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.765; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.690; Smooth: 0.900
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id6h41A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6h41A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6h41A03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (2)

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9. Files and Curves (10)