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- PDB-6kva: Structure of anti-hCXCR2 abN48-2 in complex with its CXCR2 epitope -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kva | ||||||
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Title | Structure of anti-hCXCR2 abN48-2 in complex with its CXCR2 epitope | ||||||
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![]() | IMMUNE SYSTEM / Antibody-Antigen Complex | ||||||
Function / homology | ![]() interleukin-8-mediated signaling pathway / interleukin-8 receptor activity / mast cell granule / interleukin-8 binding / C-X-C chemokine receptor activity / C-C chemokine receptor activity / C-C chemokine binding / neutrophil activation / Chemokine receptors bind chemokines / dendritic cell chemotaxis ...interleukin-8-mediated signaling pathway / interleukin-8 receptor activity / mast cell granule / interleukin-8 binding / C-X-C chemokine receptor activity / C-C chemokine receptor activity / C-C chemokine binding / neutrophil activation / Chemokine receptors bind chemokines / dendritic cell chemotaxis / cellular defense response / neutrophil chemotaxis / secretory granule membrane / G protein-coupled receptor activity / calcium-mediated signaling / receptor internalization / mitotic spindle / chemotaxis / microtubule cytoskeleton / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / cell surface receptor signaling pathway / inflammatory response / immune response / external side of plasma membrane / positive regulation of cell population proliferation / Neutrophil degranulation / cell surface / signal transduction / nucleoplasm / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xiang, J.C. / Yan, L. / Yang, B. / Wilson, I.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Selection of a picomolar antibody that targets CXCR2-mediated neutrophil activation and alleviates EAE symptoms. Authors: Shi, X. / Wan, Y. / Wang, N. / Xiang, J. / Wang, T. / Yang, X. / Wang, J. / Dong, X. / Dong, L. / Yan, L. / Li, Y. / Liu, L. / Hou, S. / Zhong, Z. / Wilson, I.A. / Yang, B. / Yang, G. / Lerner, R.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 185.8 KB | Display | ![]() |
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PDB format | ![]() | 145.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.8 KB | Display | ![]() |
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Full document | ![]() | 451.7 KB | Display | |
Data in XML | ![]() | 33.7 KB | Display | |
Data in CIF | ![]() | 49.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kvfC ![]() 4xcnS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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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Unit cell |
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Components
#1: Antibody | Mass: 24120.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 23646.229 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein/peptide | Mass: 1375.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 25% w/v Polyethylene glycol 3350 PH range: 7.0-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 42603 / % possible obs: 99.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 31 Å2 / CC1/2: 1 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4 % / Num. unique obs: 2473 / CC1/2: 0.83 / % possible all: 94.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XCN Resolution: 2.2→48.56 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.328 / ESU R Free: 0.219 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.96 Å2 / Biso mean: 32 Å2 / Biso min: 16.82 Å2
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Refinement step | Cycle: final / Resolution: 2.2→48.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.253 Å / Rfactor Rfree error: 0
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