Select a set of CDR structures?
Explore the CDR clustering?
Explore the CDR clustering in the context of other clusterings?
For each entry in SAbDab the following data is available for download:
REMARK 5 PAIRED_HL HCHAIN=B LCHAIN=A AGCHAIN=C AGTYPE=PROTEIN
REMARK 5 PAIRED_HL HCHAIN=E LCHAIN=D AGCHAIN=F AGTYPE=PROTEIN
ATOM 3877 CA SER B 82A -18.113 15.679 27.979 1.00 6.53 C
pdb Hchain Lchain model antigen_chain antigen_type ...
1ahw B A 0 C protein ...
1ahw E D 0 F protein ...
When any dataset (list of entries) is selected in SAbDab there is an option to download the data using two methods:
$ python sabdab_downloader -s summary_file.tsv -o path/to/output/ --original_pdb --imgt
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.
|PDB||The PDB accession code (e.g. 12e8)|
|Hchain||The chain identifier for the heavy chain (e.g. "H"). This is "NA" if the light chain is unpaired.|
|Lchain||The chain identifier for the light chain (e.g. "L"). This is "NA" if the heavy chain is unpaired.|
|model||The model identifier for the pairing (e.g "0","1","2"...). This is "0" for X-Ray structures )|
|antigen_chain||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 |
|antigen_type||The classification of the antigen. Either: protein, peptide, carbohydrate, nucleic acid or hapten. This is "NA" if the heavy-light pairing is unbound.|
|antigen_name||The name of the antigen. This is "NA" if heavy-light pairing is unbound or "?" if unknown.|
|short_header||The short header of the structure. Typically a short description of the type of molecule in the structure entry.|
|date||The deposition date of the structure to the PDB.|
|compound||The description of the molecule in structure. Typically the title of the associated publication.|
|organism||The organsim(s) of the molecule(s) in the structure.|
|heavy_species||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.|
|light_species||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.|
|antigen_species||The species of the antigen chain. If it is from multiple species these will be separated by a single comma.|
|authors||The authors of the structure.|
|resolution||The resolution of the structure if determined by X-Ray diffraction or Electron Microscopy.|
|method||The method with which the structure was determined.|
|r_free||The Rfree value of the structure if determined by X-Ray diffraction.|
|r_factor||The R factor value of the structure if determined by X-Ray diffraction.|
|scfv||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.|
|engineered||Whether the structure has been engineered. True or False.|
|heavy_subclass||The IMGT variable subgroup of the heavy chain. Structures that are not available in the IMGT database have a subgroup assigned by SAbDab.|
|light_subclass||The IMGT variable subgroup of the light chain. Structures that are not available in the IMGT database have a subgroup assigned by SAbDab.|
|light_ctype||The type (Kappa or Lambda) of the light chain.|
|affinity||The affinity of the antibody to the antigen present in the structure (KD - M).|
|delta_g||The ΔG of the antibody to the antigen present in the structure (kcal/mol). This has been manually calculated.|
|affinity_method||The method by which the affinity data was collected (SPR, ITC or other).|
|temperature||The temperature at which the affinity data was collected (°C).|
|pmid||The pubmed identifier that is the source of the associated affintity data.|
The relative orientation between the antibody variable domains (VH and VL) influences the topology of the antigen binding site. It is also important to consider when building high-resolution models of antibodies.
The VH-VL orientation can be characterised using six measures:
These measures have been calculated for each paired VH-VL structure in SAbDab. The distributions of a non-redundant set taken from the database can be used to visualise the VH-VL orientation space.
Selecting by angle
Selecting by PDB
Selecting by similar orientation
For a full description of the method or if you use this software, please refer to:
Dunbar et al. ABangle: characterising the VH–VL orientation in antibodies. PEDS (2013)
Light Chain (Green)
Heavy Chain (Yellow)
Warmer color means higher likelihood to be a contact with the antigen
Antibody i-Patch is a method to annotate the likelihood of antibody residues to be in contact with a given antigen. The tool can be used to annotate any Fv structure in SAbDab with respect to any antigen chain(s) in the protein data bank using the following steps: