[English] 日本語
![](img/lk-miru.gif)
- PDB-2osl: Crystal structure of Rituximab Fab in complex with an epitope peptide -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2osl | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Rituximab Fab in complex with an epitope peptide | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / Fab-peptide complex / Rituximab / chimeric antibody | ||||||
Function / homology | ![]() store-operated calcium entry / positive regulation of calcium ion import across plasma membrane / calcium ion import into cytosol / epidermal growth factor receptor binding / B cell activation / B cell proliferation / plasma membrane raft / immunoglobulin binding / humoral immune response / B cell differentiation ...store-operated calcium entry / positive regulation of calcium ion import across plasma membrane / calcium ion import into cytosol / epidermal growth factor receptor binding / B cell activation / B cell proliferation / plasma membrane raft / immunoglobulin binding / humoral immune response / B cell differentiation / protein tetramerization / response to bacterium / B cell receptor signaling pathway / MHC class II protein complex binding / cell surface receptor signaling pathway / external side of plasma membrane / cell surface / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Du, J. / Zhong, C. / Ding, J. | ||||||
![]() | ![]() Title: Structural basis for recognition of CD20 by therapeutic antibody Rituximab Authors: Du, J. / Wang, H. / Zhong, C. / Peng, B. / Zhang, M. / Li, B. / Huo, S. / Guo, Y. / Ding, J. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE Sequence database references for chain L, B and chain H, A do not currently exist. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 185.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 148.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 491.2 KB | Display | |
Data in XML | ![]() | 36 KB | Display | |
Data in CIF | ![]() | 50.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ad0S S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | the Biological Assembly is monomer. |
-
Components
#1: Antibody | Mass: 23078.623 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The protein was produced as a chimeric fab fragment. residues 1-106 is from murine and 107-213 is from human. Source: (gene. exp.) ![]() ![]() ![]() Species: , / Description: The antibody was purchased from Roche. / Production host: synthetic construct (others) #2: Antibody | Mass: 23733.541 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The protein was produced as a chimeric fab fragment. residues 1-121 is from murine and 122-224 is from human. Source: (gene. exp.) ![]() ![]() ![]() Species: , / Description: The antibody was purchased from Roche. / Production host: synthetic construct (others) #3: Protein/peptide | Mass: 2852.051 Da / Num. of mol.: 2 / Fragment: epitope peptide / Source method: obtained synthetically Details: the epitope peptide was synthesized at Shanghai Science Peptide Biological Technology Source: (synth.) ![]() #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.14 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M calcium acetate, 0.1M sodium cacodylate, 18% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 32638 / Num. obs: 29570 / % possible obs: 90.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 62.749 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Χ2: 0.892 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2 / Num. unique all: 2958 / Rsym value: 0.434 / Χ2: 0.492 / % possible all: 91.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AD0 Resolution: 2.6→43.97 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1491027.625 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.903 Å2 / ksol: 0.341 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→43.97 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|