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- PDB-8qy9: J22.9-H, fully humanized Fab Fragment based on chimeric J22.9-xi ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qy9 | |||||||||
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Title | J22.9-H, fully humanized Fab Fragment based on chimeric J22.9-xi IgG against BCMA | |||||||||
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![]() | IMMUNE SYSTEM / Fab fragment / humanized / BCMA binding | |||||||||
Function / homology | ![]() lymphocyte homeostasis / TNFs bind their physiological receptors / endomembrane system / tumor necrosis factor-mediated signaling pathway / signaling receptor activity / adaptive immune response / signal transduction / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Marino, S.F. / Daumke, O. | |||||||||
Funding support | 1items
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![]() | ![]() Title: Structure-based humanization of a therapeutic antibody for Multiple Myeloma Authors: Marino, S.F. / Daumke, O. #1: ![]() Title: Potent anti-tumor response by targeting B cell maturation antigen (BCMA) in a mouse model of multiple myeloma. Authors: Marino, S.F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 211.8 KB | Display | ![]() |
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PDB format | ![]() | 136.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430 KB | Display | ![]() |
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Full document | ![]() | 431.8 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qyaC ![]() 8qybC C: citing same article ( |
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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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Unit cell |
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Components
#1: Antibody | Mass: 23034.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Antibody | Mass: 23572.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Protein/peptide | Mass: 3741.257 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Extracellular domain of BCMA (B-cell maturation antigen, CD269) Source: (gene. exp.) ![]() ![]() ![]() | ||
#4: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.52 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 14% PEG 3350 100 mM BisTris 7.5 mM Cu(II) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→34.78 Å / Num. obs: 9584 / % possible obs: 99.19 % / Redundancy: 4.14 % / Biso Wilson estimate: 68.29 Å2 / CC1/2: 0.985 / Net I/σ(I): 6.54 |
Reflection shell | Resolution: 3.1→3.211 Å / Num. unique obs: 942 / CC1/2: 0.611 / % possible all: 99.37 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.15 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→34.78 Å
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Refine LS restraints |
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LS refinement shell |
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