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- PDB-6azk: Structure of cetuximab with aminoheptanoic acid-linked N-(3-hydro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6azk | |||||||||
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Title | Structure of cetuximab with aminoheptanoic acid-linked N-(3-hydroxypropyl)-L-arginine meditope variant | |||||||||
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![]() | IMMUNE SYSTEM / antibody / anti-EGFR | |||||||||
Function / homology | ![]() IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / 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 / 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 / adaptive immune response / Potential therapeutics for SARS / blood microparticle / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Bzymek, K.P. / Williams, J.C. | |||||||||
![]() | ![]() Title: Meditope-Fab interaction: threading the hole. Authors: Bzymek, K.P. / Ma, Y. / Avery, K.N. / Horne, D.A. / Williams, J.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 194.7 KB | Display | ![]() |
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PDB format | ![]() | 152.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.2 KB | Display | ![]() |
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Full document | ![]() | 469.1 KB | Display | |
Data in XML | ![]() | 37.2 KB | Display | |
Data in CIF | ![]() | 54.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6au5C ![]() 6axpC ![]() 6aynC ![]() 6azlC ![]() 4gw1S 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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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23287.705 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: chimeric murine/human antibody purified from Erbitux Source: (gene. exp.) ![]() ![]() ![]() Production host: unidentified (others) / References: UniProt: P01834 #2: Antibody | Mass: 23725.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: chimeric murine/human antibody purified from Erbitux Source: (gene. exp.) ![]() ![]() ![]() Production host: unidentified (others) / References: UniProt: S6B291 #3: Protein/peptide | Mass: 1450.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | Sequence of cetuximab Fab light chain in this entry matches to the sequence of cetuximab Fab light ...Sequence of cetuximab Fab light chain in this entry matches to the sequence of cetuximab Fab light chain from the first deposited cetuximab structure in PDB (1yy8) | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M citrate pH 5, 1.8 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 26, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.477→33.113 Å / Num. obs: 40781 / % possible obs: 98.8 % / Redundancy: 4.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.48→2.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 6.5 / Num. unique obs: 2690 / CC1/2: 0.954 / % possible all: 90.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4gw1 Resolution: 2.477→33.113 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 19.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.477→33.113 Å
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Refine LS restraints |
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LS refinement shell |
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