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3lb6

The structure of IL-13 in complex with IL-13Ralpha2

Method: X-RAY DIFFRACTION Dmax: 110.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Interleukin-13

Homo sapiens

UniProt P35225

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 15–146 Non-standard monomer：Yes (specific site not provided by mmCIF) Interleukin-13 receptor subunit alpha-2 × 1 （A8K7E2） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；100 mM MES, pH 6.0, 200 mM CaCl2, 20% PEG-6000, and 4% v/v polypropylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 3.05 Å R-free 0.269
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 15–146 Non-standard monomer：Yes (specific site not provided by mmCIF) Interleukin-13 receptor subunit alpha-2 × 1 （A8K7E2） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；100 mM MES, pH 6.0, 200 mM CaCl2, 20% PEG-6000, and 4% v/v polypropylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 3.05 Å R-free 0.269

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 3LB6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1GA3 NMR STRUCTURE OF INTERLEUKIN-13 Deposited 2000-11-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 35–146（112 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.1；298 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] IL-13, 25 mM phosphate buffer, 50 mM sodium chloride, 1 mM EDTA, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
1IJZ Solution Structure of Human IL-13 Deposited 2001-05-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–132（112 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 40 mM sodium phosphate, 2 mM NaN3, 40 mM NaCl；Pressure ambient
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 40 mM sodium phosphate, 2 mM NaN3, 40 mM NaCl；Pressure ambient
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 40 mM sodium phosphate, 2 mM NaN3, 40 mM NaCl；Pressure ambient
NMR sample composition 1mM interleukin-13 U-15N; 40mM phosphate buffer; 2mM NaN3; 40 mM NaCl 90% H2O, 10% D2O; pH 6.0 | 90% H2O/10% D2O
NMR sample composition 1mM interleukin-13 U-15N,U-13C; 40mM phosphate buffer; 2mM NaN3; 40 mM NaCl 90% H2O, 10% D2O; pH 6.0 | 90% H2O/10% D2O
NMR sample composition 1mM interleukin-13 U-15N,U-13C; 40mM phosphate buffer; 2mM NaN3; 40 mM NaCl; 100% D2O; pH 6.0 | 100% D2O
Resolution not provided
1IK0 Solution Structure of Human IL-13 Deposited 2001-05-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–132（112 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 40 mM sodium phosphate, 2 mM NaN3, 40 mM NaCl；Pressure ambient
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 40 mM sodium phosphate, 2 mM NaN3, 40 mM NaCl；Pressure ambient
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 40 mM sodium phosphate, 2 mM NaN3, 40 mM NaCl；Pressure ambient
NMR sample composition 1mM interleukin-13 U-15N; 40mM phosphate buffer; 2mM NaN3; 40 mM NaCl 90% H2O, 10% D2O; pH 6.0 | 90% H2O/10% D2O
NMR sample composition 1mM interleukin-13 U-15N,U-13C; 40mM phosphate buffer; 2mM NaN3; 40 mM NaCl 90% H2O, 10% D2O; pH 6.0 | 90% H2O/10% D2O
NMR sample composition 1mM interleukin-13 U-15N,U-13C; 40mM phosphate buffer; 2mM NaN3; 40 mM NaCl; 100% D2O; pH 6.0 | 100% D2O
Resolution not provided
3G6D Crystal structure of the complex between CNTO607 Fab and IL-13 Deposited 2009-02-06 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 A 21–132（112 aa） Fragment：UNP residues 21-132
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；293 K；0.1 M Sodium acetate pH 4.5, 4.9 M Sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.20 Å R-free 0.263
3G6D Crystal structure of the complex between CNTO607 Fab and IL-13 Deposited 2009-02-06 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 A 21–132（112 aa） Fragment：UNP residues 21-132
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；293 K；0.1 M Sodium acetate pH 4.5, 4.9 M Sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.20 Å R-free 0.263
3L5W Crystal structure of the complex between IL-13 and C836 FAB Deposited 2009-12-22 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 I 35–146（112 aa） Fragment：UNP residues 35-146
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；293 K；0.1 M HEPES PH 7.5, 20% PEG 3350, 0.2 M SODIUM TARTRATE; CRYO CONDITIONS: MOTHER LIQUOR + 18% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.253
3L5W Crystal structure of the complex between IL-13 and C836 FAB Deposited 2009-12-22 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 J 35–146（112 aa） Fragment：UNP residues 35-146
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；293 K；0.1 M HEPES PH 7.5, 20% PEG 3350, 0.2 M SODIUM TARTRATE; CRYO CONDITIONS: MOTHER LIQUOR + 18% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.253
3L5X Crystal structure of the complex between IL-13 and H2L6 FAB Deposited 2009-12-22 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 A 35–146（112 aa） Fragment：UNP residues 35-146
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES PH 6.5, 14% PEG 3350, 0.2 M AMMONIUM TARTRATE. CRYO CONDITIONS: 0.1 M MES PH 6.5, 20% PEG 3K, 0.2 M AMM TARTRATE, 15% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.90 Å R-free 0.247
4I77 Lebrikizumab Fab bound to IL-13 Deposited 2012-11-30 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 Z 35–146（112 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；15% w/v PEG1000, 0.05 M sodium malonate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 1.90 Å R-free 0.219
4PS4 Crystal structure of the complex between IL-13 and M1295 FAB Deposited 2014-03-06 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 A 35–146（112 aa） Fragment：UNP RESIDUES 35-146
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.1 M SODIUM ACETATE PH 4.5, 25% PEG 8K, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.80 Å R-free 0.271
5E4E Engineered Interleukin-13 bound to receptor Deposited 2015-10-05 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 34–146（113 aa） Fragment：UNP residues 34-146
Mutation：L10V, V18I, L39R, D87S, T88S, L101F, K104R, K105T SO4 SULFATE ION × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.2；293 K；lithium sulfate, phosphate/citrate pH 4.2, PEG 1000
Resolution 3.00 Å R-free 0.288
5L6Y il13 in complex with tralokinumab Deposited 2016-06-01 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 35–146（112 aa）
Not recorded FMT FORMIC ACID × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；sodium formate
Resolution 1.99 Å R-free 0.211

10 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IL13_HUMAN
Isoform —
PDB entities 1, 3
Chains and sequence ranges Author chain A； PDBConstruct 1–132； UniProt 15–146 Author chain B； PDBConstruct 1–132； UniProt 15–146

Interleukin-13 receptor subunit alpha-2

Homo sapiens

UniProt A8K7E2

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 C； UniProt 1–380 Mutation：R151Q Non-standard monomer：Yes (specific site not provided by mmCIF) Interleukin-13 × 1 （P35225） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；100 mM MES, pH 6.0, 200 mM CaCl2, 20% PEG-6000, and 4% v/v polypropylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 3.05 Å R-free 0.269
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 1–380 Mutation：R151Q Non-standard monomer：Yes (specific site not provided by mmCIF) Interleukin-13 × 1 （P35225） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；100 mM MES, pH 6.0, 200 mM CaCl2, 20% PEG-6000, and 4% v/v polypropylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 3.05 Å R-free 0.269

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A8K7E2_HUMAN
Isoform —
PDB entities 2, 4
Chains and sequence ranges Author chain C； PDBConstruct 1–380； UniProt 1–380 Author chain D； PDBConstruct 1–380； UniProt 1–380

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 3lb6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3lb6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3lb6
Deposition date deposition_date2010-01-07
Structure title titleThe structure of IL-13 in complex with IL-13Ralpha2
Keywords keywordscytokine, receptor, decoy, decoy receptor, Glycoprotein, Secreted, signaling protein-signaling protein complex; signaling protein/signaling protein
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_guinier32.18 Å
Radius of gyration Rg (electron density) rg_electron31.44 Å
Forward intensity I(0) i0111712000.00
Molecular weight molecular_weight85864.0 kDa
Excluded volume excluded_volume108180 ų
Envelope volume envelope_volume145390 ų
Hydration-shell volume shell_volume39070 ų
Envelope diameter envelope_diameter116.1 Å
Shell Rg shell_rg37.92 Å
Envelope Rg envelope_rg30.85 Å
Shape Rg shape_rg31.46 Å
Total Rg total_rg32.00 Å
Total atoms total_atoms6057
Residues n_residues751
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 dmax110.9 Å
Rg (real space) rg_real32.13 Å
Rg uncertainty (real space) rg_real_error1.01 Å
I(0) (real space) i0_real1.1170e+08
I(0) uncertainty (real space) i0_real_error1.9350e+06
Rg (reciprocal space) rg_reciprocal32.15 Å
I(0) (reciprocal space) i0_reciprocal111700000.0000
Solution quality estimate total_estimate0.8617
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary40.7 Å
Skewness Skewness skewness0.331
Kurtosis Kurtosis kurtosis-0.089
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10860000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.742; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.972
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3lb6a_
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_idd3lb6b_
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 (6 domains)

Domain ID domain_id3lb6A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3lb6B00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3lb6C01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3lb6C02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3lb6D01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3lb6D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)