Overview

Guide to Understanding PDB Data is designed to help you get started with finding and exploring the hundreds of thousands of 3D structures in the PDB archive.

If you’re new to the world of structural biology, start with Introduction to the PDB.

If you have questions about PDB data, several pages will help:

• The logic for how structures are annotated, classified, and stored is presented in Beginner’s Guide to PDBx/mmCIF Format
• The details of atomic coordinates are described in Dealing with Coordinates
• If you want to download many PDB files and/or PDB data, look at Introduction to RCSB PDB APIs

Biological molecules are complicated and diverse, and experimental techniques aren’t always perfect, so several pages describe challenges you’ll face when exploring PDB files. These include:

• Dealing with structure files with Missing Coordinates
• Ensuring that you’re exploring the functional Biological Assembly of your biomolecule
• Exploring the relationship of the Primary Sequence and the 3D structure

If you have questions about the biology of biomolecules and how it is expressed in PDB structures, explore:

• Hierarchical Structure of Proteins
• Exploring Carbohydrates
• Small Molecule Ligands

Molecular Graphics Programs offers an introduction to different ways to display biomolecules.

Many experimental and computational techniques are used to determine the structures of biomolecules.

• Experimental methods are presented in Methods for Determining Structure
• A more detailed description of X-ray crystallography is included in Crystallographic Electron Density, Resolution, and R-value
• Computation methods are presented in Computed Structure Models

Except where noted, this feature is written and illustrated by David S. Goodsell.