+
Open data
-
Basic information
Entry | Database: PDB / ID: 3l5w | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the complex between IL-13 and C836 FAB | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / immunoglobulin fold / alpha-helical bundle / Cytokine / Disulfide bond / Glycoprotein / Polymorphism / Secreted / MONOCLONAL ANTIBODY | ||||||
Function / homology | ![]() interleukin-13 receptor binding / negative regulation of lung ciliated cell differentiation / positive regulation of lung goblet cell differentiation / positive regulation of pancreatic stellate cell proliferation / regulation of proton transport / positive regulation of connective tissue growth factor production / negative regulation of complement-dependent cytotoxicity / Interleukin-18 signaling / negative regulation of transforming growth factor beta production / macrophage activation ...interleukin-13 receptor binding / negative regulation of lung ciliated cell differentiation / positive regulation of lung goblet cell differentiation / positive regulation of pancreatic stellate cell proliferation / regulation of proton transport / positive regulation of connective tissue growth factor production / negative regulation of complement-dependent cytotoxicity / Interleukin-18 signaling / negative regulation of transforming growth factor beta production / macrophage activation / positive regulation of mast cell degranulation / positive regulation of macrophage activation / positive regulation of immunoglobulin production / cellular response to cytokine stimulus / positive regulation of interleukin-10 production / negative regulation of endothelial cell apoptotic process / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of release of sequestered calcium ion into cytosol / cytokine activity / positive regulation of protein secretion / positive regulation of smooth muscle cell proliferation / microglial cell activation / response to nicotine / negative regulation of inflammatory response / cellular response to mechanical stimulus / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / response to ethanol / response to lipopolysaccharide / inflammatory response / immune response / external side of plasma membrane / positive regulation of gene expression / extracellular space / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Teplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L. | ||||||
![]() | ![]() Title: Human framework adaptation of a mouse anti-human IL-13 antibody. Authors: Fransson, J. / Teplyakov, A. / Raghunathan, G. / Chi, E. / Cordier, W. / Dinh, T. / Feng, Y. / Giles-Komar, J. / Gilliland, G. / Lollo, B. / Malia, T.J. / Nishioka, W. / Obmolova, G. / Zhao, ...Authors: Fransson, J. / Teplyakov, A. / Raghunathan, G. / Chi, E. / Cordier, W. / Dinh, T. / Feng, Y. / Giles-Komar, J. / Gilliland, G. / Lollo, B. / Malia, T.J. / Nishioka, W. / Obmolova, G. / Zhao, S. / Zhao, Y. / Swanson, R.V. / Almagro, J.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 220.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 175.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 501.7 KB | Display | |
Data in XML | ![]() | 42.9 KB | Display | |
Data in CIF | ![]() | 61.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3l5xC ![]() 3l7fC ![]() 4ps4C ![]() 1q9q C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Antibody | Mass: 23503.090 Da / Num. of mol.: 2 Fragment: CHIMERIC MOLECULE OF MOUSE VARIABLE DOMAIN AND HUMAN CONSTANT DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens Cell line (production host): Chinese hamster ovary (CHO) cells Production host: ![]() ![]() #2: Antibody | Mass: 24780.824 Da / Num. of mol.: 2 Fragment: CHIMERIC MOLECULE OF MOUSE VARIABLE DOMAIN AND HUMAN CONSTANT DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens Cell line (production host): Chinese hamster ovary (CHO) cells Production host: ![]() ![]() #3: Protein | Mass: 12490.583 Da / Num. of mol.: 2 / Fragment: UNP residues 35-146 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 48 % |
---|---|
Crystal grow | Temperature: 293 K / pH: 7.5 Details: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 31, 2008 / Details: VARIMAX HF |
Radiation | Monochromator: NONE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 76032 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2.4 / % possible all: 98.6 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1Q9Q ![]() 1q9q Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.45 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.17 / Stereochemistry target values: ENGH & HUBER
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
|