+Open data
-Basic information
Entry | Database: PDB / ID: 5fb8 | ||||||
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Title | Structure of Interleukin-16 bound to the 14.1 antibody | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Cytokine / Interleukin / Antibody / Complex | ||||||
Function / homology | Function and homology information positive regulation of interleukin-1 alpha production / induction of positive chemotaxis / CD4 receptor binding / Flemming body / leukocyte chemotaxis / Other interleukin signaling / regulation of calcium ion transport / positive regulation of interleukin-12 production / cytokine activity / positive regulation of inflammatory response ...positive regulation of interleukin-1 alpha production / induction of positive chemotaxis / CD4 receptor binding / Flemming body / leukocyte chemotaxis / Other interleukin signaling / regulation of calcium ion transport / positive regulation of interleukin-12 production / cytokine activity / positive regulation of inflammatory response / positive regulation of interleukin-6 production / nuclear speck / immune response / focal adhesion / extracellular space / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Hall, G. / Cowan, R. / Bayliss, R. / Carr, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structure of a Potential Therapeutic Antibody Bound to Interleukin-16 (IL-16): MECHANISTIC INSIGHTS AND NEW THERAPEUTIC OPPORTUNITIES. Authors: Hall, G. / Cullen, E. / Sawmynaden, K. / Arnold, J. / Fox, S. / Cowan, R. / Muskett, F.W. / Matthews, D. / Merritt, A. / Kettleborough, C. / Cruikshank, W. / Taylor, D. / Bayliss, R. / Carr, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fb8.cif.gz | 124.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fb8.ent.gz | 92.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fb8_validation.pdf.gz | 484 KB | Display | wwPDB validaton report |
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Full document | 5fb8_full_validation.pdf.gz | 491.3 KB | Display | |
Data in XML | 5fb8_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 5fb8_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/5fb8 ftp://data.pdbj.org/pub/pdb/validation_reports/fb/5fb8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 10785.303 Da / Num. of mol.: 1 / Fragment: UNP residues 1224-1323 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL16 / Plasmid: pLEICS-01 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14005 |
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-Antibody , 2 types, 2 molecules AB
#1: Antibody | Mass: 23818.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pCMV / Cell line (production host): Expi293F / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 24181.986 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pCMV / Cell line (production host): Expi293F / Production host: Homo sapiens (human) |
-Non-polymers , 4 types, 302 molecules
#4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-TRS / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 16% PEG3350, 0.1 M Bis-Tris-Propane, pH 6.5 and 0.2 M sodium sulphate. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→29.45 Å / Num. obs: 48100 / % possible obs: 99.81 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.79 |
Reflection shell | Resolution: 2.07→2.144 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 3.44 / % possible all: 99.85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I7Z for chain A, 4F33 for chain B, and 1I16 for chain C Resolution: 2.07→29.45 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.07→29.45 Å
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Refine LS restraints |
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LS refinement shell |
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