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- PDB-4lld: Structure of wild-type IgG1 antibody heavy chain constant domain ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4lld | ||||||
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Title | Structure of wild-type IgG1 antibody heavy chain constant domain 1 and light chain lambda constant domain (IgG1 CH1:Clambda) at 1.19A | ||||||
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![]() | IMMUNE SYSTEM / IgG domain / fragment of antibody | ||||||
Function / homology | ![]() IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / positive regulation of B cell activation / phagocytosis, recognition / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / positive regulation of B cell activation / phagocytosis, recognition / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / phagocytosis, engulfment / 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 / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / complement activation, classical pathway / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / 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 / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / Potential therapeutics for SARS / blood microparticle / defense response to bacterium / external side of plasma membrane / innate immune response / 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 | ![]() | 60.7 KB | Display | ![]() |
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PDB format | ![]() | 42.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.1 KB | Display | ![]() |
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Full document | ![]() | 436.7 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4llmC ![]() 4llqC ![]() 4lluC ![]() 4llwC ![]() 4llyC ![]() 3thmS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11558.932 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 13756.186 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.38 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 35% PEG 4K, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 23, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→66.925 Å / Num. all: 61588 / Num. obs: 60110 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.043 |
Reflection shell | Resolution: 1.19→1.25 Å / Rmerge(I) obs: 0.528 / % possible all: 95.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 3THM Resolution: 1.19→46.934 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.039 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.037 / 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: 15.335 Å2
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Refinement step | Cycle: LAST / Resolution: 1.19→46.934 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.19→1.221 Å / Total num. of bins used: 20
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