Specifications table

Subject area	Biochemistry
More specific subject area	Structural bioinformatics, Immunoinformatics
Type of data	A collection of atom coordinates in the pdb format, tables, text files
How data was acquired	Survey of the nanobody-antigen crystal structures deposited in the Protein Data Bank
Data format	Raw and analyzed
Experimental factors	A Protein Data Bank survey was performed in January 2018. The non-redundant data set consists of 123 structures in the pdb format. The atom coordinate files were cleaned as described below and as such may be used for further large-scale automatic analysis.
Experimental features	Nanobody CDR regions were determined using program ANARCI. Molecular surface calculations were performed using program NACCESS with the default parameters. Intermolecular contacts were found using the Biopython modules. Secondary structure of residues was assigned using DSSP as incorporated in the Biopython module “Biopdb.DSSP”.
Data source location	University of Ljubljana, Ljubljana, Slovenia
Data accessibility	Data is given in this paper.
Related research article	U. Zavrtanik, J. Lukan, R. Loris, J. Lah, S. Hadži, Structural Basis of Epitope Recognition by Heavy-Chain Camelid Antibodies, J. Mol. Biol. 430 (2018) 4369–4386. doi:10.1016/J.JMB.2018.09.002.