When any dataset (list of entries) is selected in SAbDab there is an option to download the data using two methods:
A summary file is created when a dataset is selected in SAbDab and is available for each structure individually. Each row corresponds to a heavy-light chain pairing in a PDB structure. Each pairing is annotated with the following fields.
|The PDB accession code (e.g. 12e8)
|The chain identifier for the heavy chain (e.g. "H"). This is "NA" if the light chain is unpaired.
|The chain identifier for the light chain (e.g. "L"). This is "NA" if the heavy chain is unpaired.
|The model identifier for the pairing (e.g "0","1","2"...). This is "0" for X-Ray structures )
|The chain identifier for the bound antigen chain (e.g. "A"). If the antigen has multiple bound antigen chains, these are separated by a "|" (e.g "X | Y"). For non-polymer antigens this refers to the chain identifier of the corresponding
HETATM records (i.e. it may be the same as either the heavy or light chain identifier)
|The classification of the antigen. Either: protein, peptide, carbohydrate, nucleic acid or hapten. This is "NA" if the heavy-light pairing is unbound.
HETATM of the antigen if it is non-polymer. This is "NA" if the antigen is a polymer or the heavy-light pairing is unbound.
|The name of the antigen. This is "NA" if heavy-light pairing is unbound or "?" if unknown.
|The short header of the structure. Typically a short description of the type of molecule in the structure entry.
|The deposition date of the structure to the PDB.
|The description of the molecule in structure. Typically the title of the associated publication.
|The organsim(s) of the molecule(s) in the structure.
|The species of the heavy antibody chain. If it is from multiple species (e.g. Chimeric or Humanized) these will be separated by a single comma.
|The species of the light antibody chain. If it is from multiple species (e.g. Chimeric or Humanized) these will be separated by a single comma.
|The species of the antigen chain. If it is from multiple species these will be separated by a single comma.
|The authors of the structure.
|The resolution of the structure if determined by X-Ray diffraction or Electron Microscopy.
|The method with which the structure was determined.
|The Rfree value of the structure if determined by X-Ray diffraction.
|The R factor value of the structure if determined by X-Ray diffraction.
|Whether the structure is a single chain Fv. True or False. If true, the heavy and light chain identifiers may be the same depending on how the structure has been deposited.
|Whether the structure has been engineered. True or False.
|The IMGT variable subgroup of the heavy chain. Structures that are not available in the IMGT database have a subgroup assigned by SAbDab.
|The IMGT variable subgroup of the light chain. Structures that are not available in the IMGT database have a subgroup assigned by SAbDab.
|The type (Kappa or Lambda) of the light chain.
|The affinity of the antibody to the antigen present in the structure (KD - M).
|The ΔG of the antibody to the antigen present in the structure (kcal/mol). This has been manually calculated.
|The method by which the affinity data was collected (SPR, ITC or other).
|The temperature at which the affinity data was collected (°C).
|The pubmed identifier that is the source of the associated affintity data.