Introduction to RCSB PDB’s Pairwise Alignment Tool

The Pairwise Structure Alignment Tool (https://www.rcsb.org/alignment) can align one or more protein chains to a reference structure in a pairwise manner. This tool allows for simultaneous analysis and visualization of three-dimensional (3D) structure alignments and structure-based one-dimensional (1D) sequence alignments. The two panels displaying alignment results are interconnected and selecting residues in one panel will select and highlight the same residues in the other panel. This video provides a brief introduction and demonstration.

Access the Pairwise Structure Alignment Tool from the Analyze menu at the top of the page or directly from https://www.rcsb.org/alignment.
Alignment algorithm references: https://rcsb.org/docs/tools/pairwise-...
Help Guide: https://www.rcsb.org/docs/tools/pairw...

Examples shown:
1.
Rigid comparison of mammalian tubulin (1TUB.A) and the bacterial cell division protein FtsZ (1FSZ.A): https://tinyurl.com/4z7hu3xu
Homologous proteins that play critical roles in cytoskeletal structures involved in cell division. Their three-dimensional folds are structurally similar despite relatively low sequence identity

2.
Flexible alignment of 2 calmodulin structures: calcium-free (1CLL.A) and calcium-loaded (1QX5.A): https://tinyurl.com/yck64ctb
Calmodulin consists of two globular domains (N-terminal and C-terminal lobes), each with two EF-hand motifs (calcium-binding helix-loop-helix structures). In the absence of calcium, the EF-hands are in a "closed" conformation

3.
Circular permutation alignment of Concanavalin A and peanut lectin: https://tinyurl.com/5n7zebjy
ConA and PNA are plant lectins that come from different plant sources and have distinct sugar-binding specificities.
Very similar tertiary structures, but their linear sequences are rearranged — the N- and C- termini occur at different positions in the structure compared to one another.