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Open data
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Basic information
Entry | Database: PDB / ID: 4llu | ||||||
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Title | Structure of Pertuzumab Fab with light chain Clambda at 2.16A | ||||||
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![]() | IMMUNE SYSTEM / Fab | ||||||
Function / homology | ![]() IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / immunoglobulin complex / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / immunoglobulin complex / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / antigen binding / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pustilnik, A. / Lewis, S.M. / Wu, X. / Sereno, A. / Huang, F. / Guntas, G. / Leaver-Fay, A. / Smith, E.M. / Ho, C. / Hansen-Estruch, C. ...Pustilnik, A. / Lewis, S.M. / Wu, X. / Sereno, A. / Huang, F. / Guntas, G. / Leaver-Fay, A. / Smith, E.M. / Ho, C. / Hansen-Estruch, C. / Chamberlain, A.K. / Truhlar, S.M. / Kuhlman, B. / Demarest, S.J. / Atwell, S. | ||||||
![]() | ![]() Title: Generation of bispecific IgG antibodies by structure-based design of an orthogonal Fab interface. Authors: Lewis, S.M. / Wu, X. / Pustilnik, A. / Sereno, A. / Huang, F. / Rick, H.L. / Guntas, G. / Leaver-Fay, A. / Smith, E.M. / Ho, C. / Hansen-Estruch, C. / Chamberlain, A.K. / Truhlar, S.M. / ...Authors: Lewis, S.M. / Wu, X. / Pustilnik, A. / Sereno, A. / Huang, F. / Rick, H.L. / Guntas, G. / Leaver-Fay, A. / Smith, E.M. / Ho, C. / Hansen-Estruch, C. / Chamberlain, A.K. / Truhlar, S.M. / Conner, E.M. / Atwell, S. / Kuhlman, B. / Demarest, S.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.3 KB | Display | ![]() |
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PDB format | ![]() | 138.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4lldC ![]() 4llmC ![]() 4llqC ![]() 4llwC ![]() 4llyC ![]() 1s78S 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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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 24259.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 22987.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.66 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 100mM Sodium Acetate pH 4.5 + 10% MPD + 30% PEG 2000 MME + 200mM Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 7, 2012 |
Radiation | Monochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→19.902 Å / Num. all: 52049 / Num. obs: 52049 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.175 |
Reflection shell | Resolution: 2.16→2.28 Å / Rmerge(I) obs: 0.67 / % possible all: 94.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1S78 Resolution: 2.16→19.9 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.865 / SU B: 6.206 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.981 Å2
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Refinement step | Cycle: LAST / Resolution: 2.16→19.9 Å
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