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Yorodumi- PDB-6ayn: Structure of cetuximab with aminoheptanoic acid-linked N-(3-amino... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ayn | ||||||||||||
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Title | Structure of cetuximab with aminoheptanoic acid-linked N-(3-aminopropyl)-L-arginine meditope variant | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody / anti-EGFR | ||||||||||||
Function / homology | Function and homology information 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 / complement activation, classical pathway / 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 / antibacterial humoral response / Potential therapeutics for SARS / adaptive immune response / blood microparticle / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.48 Å | ||||||||||||
Authors | Bzymek, K.P. / Williams, J.C. | ||||||||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ayn.cif.gz | 192.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ayn.ent.gz | 150.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ayn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ayn_validation.pdf.gz | 450.3 KB | Display | wwPDB validaton report |
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Full document | 6ayn_full_validation.pdf.gz | 454.5 KB | Display | |
Data in XML | 6ayn_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 6ayn_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/6ayn ftp://data.pdbj.org/pub/pdb/validation_reports/ay/6ayn | HTTPS FTP |
-Related structure data
Related structure data | 6au5C 6axpC 6azkC 6azlC 4gw1S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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 Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Plasmid details: purified from commercial source erbitux, expression host unknown Gene: IGKC / 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 Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Plasmid details: purified from commercial source erbitux, expression host unknown Production host: unidentified (others) / References: UniProt: S6B291 #3: Protein/peptide | Mass: 1449.741 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M citrate pH 5, 1.6 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 1, 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: 2.48→33.121 Å / Num. obs: 40771 / % possible obs: 99 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 2.48→2.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 2714 / CC1/2: 0.921 / % possible all: 91 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4gw1 Resolution: 2.48→33.121 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 20.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.48→33.121 Å
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Refine LS restraints |
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LS refinement shell |
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