Diagrams illustrating the correspondence between a given structural model and the full-length sequence of the corresponding protein. (a) A schematic Pfam diagram taken from the PDBsum atlas page for PDB entry 1t5i: human pre-mRNA-processing protein (15). The extent of the 3D structural model is shown beneath the Pfam domains and shows that the structural model corresponds to only the C-terminal helicase C domain. Clicking on the orange ‘+’ icon returns all other PDB entries for the given UniProt sequence (UAP56_HUMAN). (b) The top five PDB entries for this sequence. From this one can see that, in addition to the 1t5i partial structural model of this protein shown in (a) (listed here at position 5), there are three models of the complete protein and one model of just the N-terminal domain.

Schematic diagrams from the PDBsum ‘Protein page’ for entry 1a5z: lactate dehydrogenase from Thermatoga maritima (16). (a) The ‘wiring diagram’ shows the protein's secondary structure elements (α-helices and β-sheets) together with various structural motifs such as β- and γ-turns, and β-hairpins. The yellow linking bars labelled 1 and 2 represent disulphide bonds. The single-letter amino acid codes showing the protein's sequence are coloured red or blue depending on whether they belong to CATH structural domain 1 or 2, respectively. Catalytic residues are indicated by a box surrounding the amino acid code. Red dots above the single-letter codes signify residues that interact with any bound ligand(s) while coloured lines underneath represent residues belonging to a PROSITE pattern, the redder the colour the more highly conserved the residue in the pattern. (b) Topology diagram of the first (i.e. red) structural domain in 1a5z. The diagram illustrates how the β-strands, represented by the large arrows, join up, side-by-side, to form the domain's central β-sheet. The diagram also shows the relative locations of the α-helices, here represented by the red cylinders. The small arrows indicate the directionality of the protein chain, from the N- to the C-terminus. The numbers within the secondary structural elements correspond to the residue numbering given in the PDB file.

Extracts from the protein–protein interaction diagrams in PDBsum for PDB entry 1mmo, a non-haem iron hydroxylase from Methylococcus capsulatus (17). (a) Thumbnail image of the 3D structural model which contains six protein chains: two of MEMB_METCA (chains B and C), two of MEMB_METCA (chains D and E) and two of MEMG_METCA (chains G and H). (b) Schematic diagram showing the interactions between the chains. The area of each circle is proportional to the surface area of the corresponding protein chain. The extent of the interface region on each chain is represented by a coloured wedge whose colour corresponds to the colour of the other chain and whose size signifies the interface surface area. The joining lines are coloured light blue for hydrogen bonds and orange for non-bonded contacts. (c) A schematic diagram showing the numbers of interactions across one of the interfaces, namely the B–G interface, and the numbers of residues involved. (d) Detail of the individual residue–residue interactions across this interface. The colour of the interactions is as above.