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Open data
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Basic information
Entry | Database: PDB / ID: 8df1 | ||||||
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Title | Chi3l1 bound by antibody C59 | ||||||
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![]() | IMMUNE SYSTEM / Chi3l1 / Fab / immunotherapeutic | ||||||
Function / homology | ![]() response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / cartilage development / chitin catabolic process / extracellular matrix structural constituent / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / extracellular matrix ...response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / cartilage development / chitin catabolic process / extracellular matrix structural constituent / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / extracellular matrix / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / lung development / specific granule lumen / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate binding / carbohydrate metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / inflammatory response / apoptotic process / Neutrophil degranulation / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wrapp, D. / McLellan, J.S. | ||||||
Funding support | 1items
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![]() | ![]() Title: A novel humanized Chi3l1 blocking antibody attenuates acetaminophen-induced liver injury in mice. Authors: Li, L. / Wen, Y. / Wrapp, D. / Jeong, J. / Zhao, P. / Xiong, W. / Atkins, C.L. / Shan, Z. / Hui, D. / McLellan, J.S. / Zhang, N. / Ju, C. / An, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.8 MB | Display | ![]() |
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PDB format | ![]() | 1.5 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 156.1 KB | Display | |
Data in CIF | ![]() | 212 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4hbcS ![]() 4p8vS ![]() 6pehS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 40536.758 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Antibody , 2 types, 12 molecules MHOQSUNLPRTV
#2: Antibody | Mass: 23486.350 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Antibody | Mass: 22719.049 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 3 types, 6 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.14 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH 8.5, 10% PEG 4000, 2% MPD |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→87.29 Å / Num. obs: 108604 / % possible obs: 99.86 % / Redundancy: 11.8 % / Biso Wilson estimate: 56.88 Å2 / Rmerge(I) obs: 0.796 / Net I/σ(I): 8.97 |
Reflection shell | Resolution: 3.3→3.418 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 1.87 / Num. unique obs: 10701 / CC1/2: 0.421 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4P8V, 6PEH, 4HBC Resolution: 3.3→87.29 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso max: 241.48 Å2 / Biso mean: 71.1652 Å2 / Biso min: 21.74 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→87.29 Å
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