A global survey of intramolecular isopeptide bonds

Data for "A global survey of intramolecular isopeptide bonds" Francesco Costa1, Ioannis Riziotis1, Antonina Andreeva1, Delhi Kalwan2, Jennifer de Jong2, Philip Hinchliffe3, Fabio Parmeggiani2,4,5, Paul R. Race2,6, Steven G. Burston2, Alex Bateman1, Rob Barringer2 1 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton. CB10 1SD. UK 2 School of Biochemistry, University of Bristol, University Walk, Bristol. BS8 1TD. UK 3 School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol, BS8 1TD, UK. 4 School of Chemistry, University of Bristol, Cantock’s Close, Bristol. BS8 1TS. UK 5 School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, Cardiff. CF10 3NB , UK 6 School of Natural and Environmental Sciences, Devonshire Building, Newcastle University, Newcastle upon Tyne. NE1 7RU. UK The following files are present: - afdb_scan_isopeptor.csv and bfvd_scan_isopeptor.csv contain the results of isopeptor scans across AFDB and BFVD databases. Columns: - uniprot_acc: uniprot accession code - probability: isopeptor's probability of isopeptide bond - r{1_bond,_cat,2_bond}: position of respectively the first bonded residue, the catalytic residue and the second bonded residue; - r{1_bond,_cat,2_bond}: name of respectively the first bonded residue, the catalytic residue and the second bonded residue; - bond_type: CnaA-like or CnaB-like classification; - rmsd: root mean square deviation with the closest matching template expressed in Angstrom; - r_asa: average relative accessible solvent area of the three isopeptide bond residues; - template: name of the closest structural template; - pfamA_acc,pfamA_id,clan_acc,clan_id: pfam domain accession code, name, clan accession code and name of the domain which matches the region of the isopeptide bond; - seq_start,seq_end: pfam domain sequence start and end; - taxonomy,species,kingdom: taxonomy, species and superkingdom annotations; - r{1,2,3}_plddt: plddt of respectively the first bonded residue, the catalytic residue and the second bonded residue;- pdb_isopeptide_models_biochemical_analysis.csv and af2_isopeptide_models_biochemical_analysis.csv contain the biochemical analysis performed on the dataset of intramolecular isopeptide bond structures. Note that the original table was derived from Costa et al., 2025 and that structures of re-modelled isopeptide bonds are available in the following public repository: https://github.com/FranceCosta/Isopeptor_development Common columns: - PDB code - Chain - UniProt Id - Species - Name: protein name - Position 1 (Bond 1) - Residue 1: residue name - Position 2 (catalytic) - Residue 2 - Position 3 (Bond 2) - Residue 3 - Isopeptide type: CnaA-like, CnaB-like or mutant; - Domain insert in loop? - Insertion name? - Reference - Bad rotamer: assigned to isopeptide bonds which have been not modelled correctly and which were not re-modelled due to the lack of electron density maps (data from Costa et al., 2025); - Deposition date - Fixed: indicates if the isopeptide bond structure has been remodelled; - Resolution - Unusual geometry/chemistry: indicates cases of unusual geometry or chemistry of the isopeptide bond (e.g. incomplete or missing sidechains, present on a flexible loops etc.) - bond_length - pseudo_omega - pseudo_psi - pseudo_phi Columns only present in pdb_isopeptide_models_biochemical_analysis.csv: - aro_res_id: residue number of the closest aromatic residue within a radius of 10 Å from the isopeptide bond NZ atom; - aro_res_name: residue name of the closest aromatic residue within a radius of 10 Å from the isopeptide bond NZ atom; - distance_to_aro: distance between isopeptide bond NZ atom and the centroid of the aromatic residue ring (the closer ring is considered for trypthophan) - aro_plane_normal-isopep_NZ_angle: angle between the isopeptide bond NZ atom vector and the aromatic plane normal; - aro_cap: if the aromatic residue forms an "aromatic cap" with the isopeptide bond (distance within 6 Å and angle <30° or >150°); - water_resid_OD: residue number of closest water molecule within a radius of 5 Å from the isopeptide bond OD atom; - water_distance_OD: water molecule distance to isopeptide bond OD atom; - o_atom_ref: reference of closest O atom to the isopeptide bond OD atom (within a radius of 5 Å) - o_atom_distance: distance of closest O atom to isopeptide bond OD atom (within a radius of 5 Å); - rASA: per-residue relative solvent accessible area - cis_trans: if the bond is in a cis (pseudo_omega angle < 60) or trans (pseudo_omega angle > 120) conformation; Columns only present in af2_isopeptide_models_biochemical_analysis.csv: - r{1,2,3}_af: position of respectively the first bonded residue, the catalytic residue and the second bonded residue in the AlphaFold model; - afdb_scan_isopeptor_pfam_annotations.csv contains all the Pfam domain annotations of the proteins detected by isopeptor in the AFDB scan;- fa_pred.csv contains the results of the fibrillar adhesin prediction;- alphafold2_models.zip.gz contains the compressed results of AlphaFold2 modelling described in this study;- afdb_bacteria_random_sequences.csv and afdb_archaea_random_sequences.csv contain randomly selected protein uniprot acession code, length and taxonomy of Bacteria and Archaea extracted from the AFDB and used in this study; References: Costa,F. et al. (2025) Isopeptor: a tool for detecting intramolecular isopeptide bonds in protein structures. Bioinformatics Advances, vbaf049. For questions, contact:Francesco CostaEmail: [email protected]