3l5w

Crystal structure of the complex between IL-13 and C836 FAB

Method: X-RAY DIFFRACTION Dmax: 148.8 Å Quality: GOOD

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain I; UniProt 35–146 Fragment:UNP residues 35-146 C836 LIGHT CHAIN × 1 C836 HEAVY CHAIN × 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
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain J; UniProt 35–146 Fragment:UNP residues 35-146 C836 LIGHT CHAIN × 1 C836 HEAVY CHAIN × 1 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

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.

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 3
Chains and sequence ranges Author chain I; PDBConstruct 2–113; UniProt 35–146 Author chain J; PDBConstruct 2–113; UniProt 35–146

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 3l5w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3l5w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3l5w
Deposition date deposition_date2009-12-22
Structure title titleCrystal structure of the complex between IL-13 and C836 FAB
Keywords keywords;immunoglobulin fold, alpha-helical bundle, Cytokine, Disulfide bond, Glycoprotein, Polymorphism, Secreted, MONOCLONAL ANTIBODY, IMMUNE SYSTEM ;; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.33
Radius of gyration Rg (electron density) rg_electron41.46
Forward intensity I(0) i0197559000.00
Molecular weight molecular_weight114820.0 kDa
Excluded volume excluded_volume143910 ų
Envelope volume envelope_volume197560 ų
Hydration-shell volume shell_volume41690 ų
Envelope diameter envelope_diameter157.1
Shell Rg shell_rg43.76
Envelope Rg envelope_rg41.18
Shape Rg shape_rg41.42
Total Rg total_rg41.75
Total atoms total_atoms8079
Residues n_residues1057
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax148.8
Rg (real space) rg_real41.63
Rg uncertainty (real space) rg_real_error1.90
I(0) (real space) i0_real1.9760e+08
I(0) uncertainty (real space) i0_real_error4.1000e+06
Rg (reciprocal space) rg_reciprocal41.33
I(0) (reciprocal space) i0_reciprocal197500000.0000
Solution quality estimate total_estimate0.8387
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary47.0
Skewness Skewness skewness0.537
Kurtosis Kurtosis kurtosis-0.046
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13860000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.770; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.869; Smooth: 0.721

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd3l5wa1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd3l5wa2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd3l5wb_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd3l5wh_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd3l5wi_
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_idd3l5wj_
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_idd3l5wl1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd3l5wl2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (10 domains)

Domain ID domain_id3l5wA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3l5wA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3l5wB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3l5wB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3l5wH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3l5wH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3l5wI00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily10
Domain ID domain_id3l5wJ00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily10
Domain ID domain_id3l5wL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3l5wL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)