LigASite--a database of biologically relevant binding sites in proteins with known apo-structures

Abstract

Better characterization of binding sites in proteins and the ability to accurately predict their location and energetic properties are major challenges which, if addressed, would have many valuable practical applications. Unfortunately, reliable benchmark datasets of binding sites in proteins are still sorely lacking. Here, we present LigASite ('LIGand Attachment SITE'), a gold-standard dataset of binding sites in 550 proteins of known structures. LigASite consists exclusively of biologically relevant binding sites in proteins for which at least one apo- and one holo-structure are available. In defining the binding sites for each protein, information from all holo-structures is combined, considering in each case the quaternary structure defined by the PQS server. LigASite is built using simple criteria and is automatically updated as new structures become available in the PDB, thereby guaranteeing optimal data coverage over time. Both a redundant and a culled non-redundant version of the dataset is available at http://www.scmbb.ulb.ac.be/Users/benoit/LigASite. The website interface allows users to search the dataset by PDB identifiers, ligand identifiers, protein names or sequence, and to look for structural matches as defined by the CATH homologous superfamilies. The datasets can be downloaded from the website as Schema-validated XML files or comma-separated flat files.

Figure 1.

Flow-chart summarizing the automated procedure to generate LigASite from the PDB.

Figure 2.

Turkey egg-white lysozyme. (a) Mapping of binding site residues on the apo-structure (PDB entry 135l). These residues are identified as part of the binding site from the three holo-structures in which the lysozyme is in complex with different ligands: (b) with three molecules of N-acetyl-d-glucosamine (NAG) and a sulphate ion in PDB entry 1jef; (c) with di(N-acetyl-d-glucosamine) in PDB entry 1ljn; and (d) with two molecules of NAG in PDB entry 1lzy. Binding site residues are coloured red if they are in contact with ligand atoms in all three holo-structures (i.e. frequency score of 1.0 = 3/3), they are coloured orange if they are only in contact with ligand atoms in two of the holo-structures (i.e. frequency score of 0.67 ≈ 2/3), and they are coloured yellow if they are in contact with ligand atoms in only one holo-structure (i.e. frequency score of 0.33 ≈ 1/3). HET-groups considered as biologically relevant in LigASite are displayed and coloured in CPK. Sulphate ions filtered out as biologically irrelevant in PDB entry 1ljn are transparent and displayed in balls-and-sticks. The figure was drawn with molscript (27) and rendered with Raster3D (28).

Figure 3.

Distribution of EC classes among proteins in (a) the non-redundant version of the LigASite dataset (redundancy removed at 25% sequence identity), and in (b) a non-redundant subset of the PDB (redundancy removed at 25% sequence identity), which consists of 5180 PDB entries. EC numbers were obtained from PDBSprotEC, a mapping of PDB entries to EC numbers via SwissProt (26).