RCSB PDB web portal RCSB.org for biotechnology research: exploration and visualization of plastic-degrading enzymes at the atomic level in 3D

Introduction The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) develops resources for biomolecular structure exploration and analysis that are used by an interdisciplinary community of bio scientists, researchers, and students numbering in the many millions worldwide. The RCSB.org website and suite of APIs provide access to more than 250,000 experimentally determined structures archived in the PDB, making it an invaluable tool for biotechnology, such as research on plastic-degrading enzymes. Engineering plastic-degrading enzymes represents a promising strategy for mitigating environmental accumulation of polyethylene terephthalate (PET). Methods In recent years, RCSB.org has provided access to more than 1 million Computed Structure Models (CSMs) alongside experimentally determined structures and introduced new tools for 3D Motif Search, Visualizing Sequence Annotations in 3D, and Pairwise Structure Alignment. Results and discussion To identify site-directed mutagenesis targets for improving PET-degrading enzyme efficiency, biotechnology researchers utilize 3D structure data freely available from the PDB. This article describes how RCSB PDB tools for Advanced Search, Visualizing Sequence Annotations in 3D, and Pairwise Structure Alignment can be used to study plastic-degrading enzyme structure and function.