Guide to Understanding PDB Data: Hierarchical Structure
Atomic representations are shown at left, and cartoon representations are shown at left. Alpha helices form spring-shaped structures with each amino acid forming a hydrogen bond with an amino acid further down the chain. Beta strands are extended regions of the chain that form hydrogen bonds with neighboring beta strands, forming a beta sheet. In this structure, four beta strands form the sheet with neighboring strands running in opposite directions, as shown by the cartoon arrows. Note that in these illustrations, side chains are not shown on each amino acid, to make it easier to see the backbone structure. Structures taken from PDB ID 1ic2 and 4gcr.
The constantly-growing PDB is a reflection of the research that is happening in laboratories across the world. This can make it both exciting and challenging to use the database in research and education.
PDB-101 helps teachers, students, and the general public explore the 3D world of proteins and nucleic acids. Learning about their diverse shapes and functions helps to understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease to biological energy.
Why PDB-101? Researchers around the globe make these 3D structures freely available at the Protein Data Bank (PDB) archive. PDB-101 builds introductory materials to help beginners get started in the subject ("101", as in an entry level course) as well as resources for extended learning.