Guide to Understanding PDB Data
Introduction
PDB Overview
Protein Hierarchical Structure
Beginner’s Guide to PDBx/mmCIF
Missing Coordinates and Biological Assemblies
Dealing with Coordinates
Primary Sequences
Biological Assemblies
Computed Structure Models
Small Molecule Ligands
Exploring Carbohydrates
Methods for Determining Structure
Crystallographic Structure Factors and Electron Density, Resolution, and R-value
Molecular Graphics Programs
Introduction to RCSB PDB APIs

PDB Overview

Founded in 1971, the Protein Data Bank (PDB) archive is a repository of atomic coordinates and other information describing proteins and other important biological macromolecules. Structural biologists studying proteins and nucleic acids deposit atomic coordinates and information associated with the experiment to the PDB, which is then annotated by wwPDB biocurators and publicly released into the public archive.

In addition to the experimentally-determined 3D structures that are archived in the PDB, RCSB PDB provides access to protein structures predicted by computational methods (Computed Structure Models).

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. Structures are available for many of the proteins and nucleic acids involved in the central processes of life, so you can go to the PDB archive to find structures for ribosomes, oncogenes, drug targets, and even whole viruses. You may find multiple structures for a given molecule, or partial structures, or structures that have been modified or inactivated from their native form.

This Guide to Understanding PDB Data is designed to help you get started with charting a path through this material, and help you avoid a few common pitfalls. These chapters are intertwined with one another. To begin, choose a topic from the menu on the left, or select a topic linked below:

PDB Data

The information stored in the PDB archive primarily consists of coordinate files. These files list the atoms contained in the biological molecules studied and their 3D locations in space. These files are available in PDBx/mmCIF and PDBML/XML format. A typical PDBx/mmCIF formatted file also contains information that summarizes the identity of the protein, citation information, details of the structure determination, details about primary and secondary structure, as well as information about ligands and carbohydrates included in the entry.

The PDBx/mmCIF file is built using an underlying dictionary structure for annotation, classification, presentation, and storage.

The RCSB PDB website uses APIs to access these PDBx/mmCIF data in an automated way.

Visualizing Structures

Online visualization tools at RCSB.org such as Mol* allow you to display information about a structure on your computer and create custom images. These programs also often include analysis tools that allow you to measure distances and bond angles, and identify interesting structural features.

Reading Coordinate Files

When you start exploring the structures in the PDB archive, you will need to know a few things about the coordinates. In a typical entry, you will find a diverse mixture of biological molecules, small molecules, ions, and water. Often, you can use the names and chain IDs to help sort these out. In structures determined from crystallography, atoms are annotated with temperature factors that describe their vibration and occupancies that show if they are seen in several conformations. NMR structures often include several different models of the molecule.

Potential Challenges

You may run into several challenges as you explore the PDB archive. For example, many structures, particular those determined by crystallography, only include information about part of the functional biological assembly. Also, many PDB entries are missing portions of the molecule that were not observed in the experiment. These include structures that include only alpha carbon positions, structures with missing loops, structures of individual domains, or subunits from a larger molecule. In addition, most of the crystallographic structure entries do not have information on hydrogen atoms. Using this Guide will help you better utilize PDB data in your research and training.

The Guide to Understanding PDB Data is updated along with major enhancements to RCSB.org and the PDB archive, such as the transition to extended PDB IDs and major remediation efforts (e.g., carbohydrates).

Contact PDB-101 with suggestions for new topic areas.